Date: 2019-12-25 20:17:13 CET, cola version: 1.3.2
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All available functions which can be applied to this res_list object:
res_list
#> A 'ConsensusPartitionList' object with 24 methods.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows are extracted by 'SD, CV, MAD, ATC' methods.
#> Subgroups are detected by 'hclust, kmeans, skmeans, pam, mclust, NMF' method.
#> Number of partitions are tried for k = 2, 3, 4, 5, 6.
#> Performed in total 30000 partitions by row resampling.
#>
#> Following methods can be applied to this 'ConsensusPartitionList' object:
#> [1] "cola_report" "collect_classes" "collect_plots" "collect_stats"
#> [5] "colnames" "functional_enrichment" "get_anno_col" "get_anno"
#> [9] "get_classes" "get_matrix" "get_membership" "get_stats"
#> [13] "is_best_k" "is_stable_k" "ncol" "nrow"
#> [17] "rownames" "show" "suggest_best_k" "test_to_known_factors"
#> [21] "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single method by, e.g. object["SD", "hclust"] or object["SD:hclust"]
#> or a subset of methods by object[c("SD", "CV")], c("hclust", "kmeans")]
The call of run_all_consensus_partition_methods() was:
#> run_all_consensus_partition_methods(data = mat, mc.cores = 4, anno = anno)
Dimension of the input matrix:
mat = get_matrix(res_list)
dim(mat)
#> [1] 11993 171
The density distribution for each sample is visualized as in one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.
library(ComplexHeatmap)
densityHeatmap(mat, top_annotation = HeatmapAnnotation(df = get_anno(res_list),
col = get_anno_col(res_list)), ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 4)
Folowing table shows the best k (number of partitions) for each combination
of top-value methods and partition methods. Clicking on the method name in
the table goes to the section for a single combination of methods.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_list)
| The best k | 1-PAC | Mean silhouette | Concordance | ||
|---|---|---|---|---|---|
| SD:kmeans | 2 | 1.000 | 0.992 | 0.996 | ** |
| SD:skmeans | 2 | 1.000 | 0.968 | 0.987 | ** |
| SD:pam | 2 | 1.000 | 0.985 | 0.994 | ** |
| CV:kmeans | 2 | 1.000 | 0.964 | 0.985 | ** |
| CV:skmeans | 2 | 1.000 | 0.964 | 0.985 | ** |
| MAD:skmeans | 2 | 1.000 | 0.975 | 0.990 | ** |
| MAD:pam | 2 | 1.000 | 0.969 | 0.987 | ** |
| ATC:kmeans | 2 | 1.000 | 0.996 | 0.998 | ** |
| ATC:skmeans | 2 | 1.000 | 0.984 | 0.994 | ** |
| ATC:pam | 2 | 1.000 | 0.980 | 0.992 | ** |
| ATC:mclust | 2 | 1.000 | 0.993 | 0.997 | ** |
| MAD:kmeans | 2 | 0.989 | 0.966 | 0.985 | ** |
| MAD:NMF | 2 | 0.987 | 0.964 | 0.984 | ** |
| MAD:mclust | 2 | 0.949 | 0.945 | 0.969 | * |
| CV:NMF | 2 | 0.927 | 0.939 | 0.974 | * |
| SD:NMF | 2 | 0.926 | 0.933 | 0.971 | * |
| CV:mclust | 4 | 0.870 | 0.900 | 0.937 | |
| ATC:NMF | 3 | 0.747 | 0.855 | 0.929 | |
| CV:hclust | 2 | 0.730 | 0.922 | 0.945 | |
| SD:hclust | 2 | 0.722 | 0.913 | 0.939 | |
| SD:mclust | 4 | 0.663 | 0.817 | 0.888 | |
| ATC:hclust | 5 | 0.466 | 0.717 | 0.842 | |
| CV:pam | 3 | 0.426 | 0.757 | 0.823 | |
| MAD:hclust | 2 | 0.409 | 0.697 | 0.860 |
**: 1-PAC > 0.95, *: 1-PAC > 0.9
Cumulative distribution function curves of consensus matrix for all methods.
collect_plots(res_list, fun = plot_ecdf)
Consensus heatmaps for all methods. (What is a consensus heatmap?)
collect_plots(res_list, k = 2, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 3, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 4, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 5, fun = consensus_heatmap, mc.cores = 4)
collect_plots(res_list, k = 6, fun = consensus_heatmap, mc.cores = 4)
Membership heatmaps for all methods. (What is a membership heatmap?)
collect_plots(res_list, k = 2, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 3, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 4, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 5, fun = membership_heatmap, mc.cores = 4)
collect_plots(res_list, k = 6, fun = membership_heatmap, mc.cores = 4)
Signature heatmaps for all methods. (What is a signature heatmap?)
Note in following heatmaps, rows are scaled.
collect_plots(res_list, k = 2, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 3, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 4, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 5, fun = get_signatures, mc.cores = 4)
collect_plots(res_list, k = 6, fun = get_signatures, mc.cores = 4)
The statistics used for measuring the stability of consensus partitioning. (How are they defined?)
get_stats(res_list, k = 2)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 2 0.926 0.933 0.971 0.459 0.535 0.535
#> CV:NMF 2 0.927 0.939 0.974 0.472 0.526 0.526
#> MAD:NMF 2 0.987 0.964 0.984 0.473 0.523 0.523
#> ATC:NMF 2 0.893 0.932 0.971 0.425 0.574 0.574
#> SD:skmeans 2 1.000 0.968 0.987 0.482 0.518 0.518
#> CV:skmeans 2 1.000 0.964 0.985 0.483 0.518 0.518
#> MAD:skmeans 2 1.000 0.975 0.990 0.484 0.518 0.518
#> ATC:skmeans 2 1.000 0.984 0.994 0.481 0.521 0.521
#> SD:mclust 2 0.888 0.965 0.982 0.317 0.701 0.701
#> CV:mclust 2 0.693 0.924 0.943 0.332 0.701 0.701
#> MAD:mclust 2 0.949 0.945 0.969 0.328 0.694 0.694
#> ATC:mclust 2 1.000 0.993 0.997 0.287 0.717 0.717
#> SD:kmeans 2 1.000 0.992 0.996 0.318 0.687 0.687
#> CV:kmeans 2 1.000 0.964 0.985 0.318 0.687 0.687
#> MAD:kmeans 2 0.989 0.966 0.985 0.337 0.673 0.673
#> ATC:kmeans 2 1.000 0.996 0.998 0.313 0.687 0.687
#> SD:pam 2 1.000 0.985 0.994 0.302 0.701 0.701
#> CV:pam 2 0.709 0.922 0.945 0.327 0.694 0.694
#> MAD:pam 2 1.000 0.969 0.987 0.319 0.694 0.694
#> ATC:pam 2 1.000 0.980 0.992 0.292 0.709 0.709
#> SD:hclust 2 0.722 0.913 0.939 0.344 0.701 0.701
#> CV:hclust 2 0.730 0.922 0.945 0.333 0.701 0.701
#> MAD:hclust 2 0.409 0.697 0.860 0.399 0.574 0.574
#> ATC:hclust 2 0.499 0.839 0.920 0.329 0.694 0.694
get_stats(res_list, k = 3)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 3 0.640 0.757 0.885 0.420 0.670 0.453
#> CV:NMF 3 0.469 0.622 0.807 0.375 0.706 0.491
#> MAD:NMF 3 0.558 0.676 0.847 0.390 0.689 0.470
#> ATC:NMF 3 0.747 0.855 0.929 0.496 0.677 0.485
#> SD:skmeans 3 0.833 0.873 0.945 0.389 0.772 0.577
#> CV:skmeans 3 0.664 0.787 0.901 0.381 0.720 0.504
#> MAD:skmeans 3 0.827 0.864 0.940 0.380 0.794 0.611
#> ATC:skmeans 3 0.879 0.874 0.951 0.373 0.721 0.509
#> SD:mclust 3 0.502 0.776 0.827 0.748 0.729 0.616
#> CV:mclust 3 0.450 0.689 0.831 0.703 0.667 0.530
#> MAD:mclust 3 0.515 0.831 0.865 0.712 0.736 0.624
#> ATC:mclust 3 0.887 0.908 0.955 1.103 0.678 0.551
#> SD:kmeans 3 0.809 0.925 0.943 0.900 0.669 0.525
#> CV:kmeans 3 0.602 0.838 0.871 0.844 0.665 0.521
#> MAD:kmeans 3 0.755 0.879 0.931 0.832 0.658 0.507
#> ATC:kmeans 3 0.790 0.885 0.915 0.932 0.666 0.517
#> SD:pam 3 0.549 0.743 0.835 0.979 0.699 0.575
#> CV:pam 3 0.426 0.757 0.823 0.789 0.701 0.575
#> MAD:pam 3 0.509 0.665 0.820 0.901 0.699 0.570
#> ATC:pam 3 0.634 0.839 0.916 0.990 0.705 0.588
#> SD:hclust 3 0.511 0.754 0.877 0.335 0.894 0.849
#> CV:hclust 3 0.413 0.649 0.864 0.323 0.990 0.986
#> MAD:hclust 3 0.339 0.603 0.768 0.286 0.946 0.906
#> ATC:hclust 3 0.496 0.653 0.833 0.394 0.768 0.681
get_stats(res_list, k = 4)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 4 0.562 0.591 0.788 0.1092 0.840 0.595
#> CV:NMF 4 0.499 0.536 0.749 0.1177 0.777 0.468
#> MAD:NMF 4 0.537 0.579 0.766 0.1065 0.838 0.593
#> ATC:NMF 4 0.787 0.827 0.920 0.0730 0.829 0.595
#> SD:skmeans 4 0.884 0.878 0.936 0.1104 0.906 0.724
#> CV:skmeans 4 0.604 0.695 0.807 0.1143 0.885 0.672
#> MAD:skmeans 4 0.811 0.832 0.911 0.1117 0.916 0.751
#> ATC:skmeans 4 0.854 0.899 0.945 0.1230 0.785 0.468
#> SD:mclust 4 0.663 0.817 0.888 0.2053 0.874 0.718
#> CV:mclust 4 0.870 0.900 0.937 0.1964 0.923 0.803
#> MAD:mclust 4 0.673 0.833 0.901 0.1946 0.890 0.753
#> ATC:mclust 4 0.714 0.787 0.814 0.1712 0.774 0.488
#> SD:kmeans 4 0.626 0.369 0.610 0.1520 0.878 0.714
#> CV:kmeans 4 0.574 0.613 0.789 0.1747 0.740 0.444
#> MAD:kmeans 4 0.635 0.687 0.774 0.1461 0.799 0.514
#> ATC:kmeans 4 0.645 0.751 0.784 0.1680 0.798 0.509
#> SD:pam 4 0.597 0.768 0.809 0.0874 0.951 0.886
#> CV:pam 4 0.512 0.738 0.808 0.1192 0.951 0.886
#> MAD:pam 4 0.469 0.581 0.713 0.1113 0.957 0.898
#> ATC:pam 4 0.632 0.776 0.834 0.0442 0.991 0.980
#> SD:hclust 4 0.460 0.717 0.836 0.1500 0.961 0.934
#> CV:hclust 4 0.400 0.672 0.812 0.1776 0.877 0.823
#> MAD:hclust 4 0.388 0.542 0.725 0.1513 0.815 0.666
#> ATC:hclust 4 0.483 0.689 0.836 0.0571 0.985 0.971
get_stats(res_list, k = 5)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 5 0.549 0.576 0.745 0.0759 0.850 0.548
#> CV:NMF 5 0.557 0.621 0.758 0.0781 0.874 0.596
#> MAD:NMF 5 0.548 0.494 0.722 0.0758 0.851 0.553
#> ATC:NMF 5 0.564 0.659 0.794 0.0654 0.953 0.858
#> SD:skmeans 5 0.777 0.796 0.874 0.0727 0.907 0.663
#> CV:skmeans 5 0.684 0.700 0.826 0.0718 0.877 0.576
#> MAD:skmeans 5 0.723 0.690 0.815 0.0704 0.905 0.654
#> ATC:skmeans 5 0.817 0.829 0.905 0.0600 0.917 0.697
#> SD:mclust 5 0.689 0.640 0.763 0.0968 0.862 0.602
#> CV:mclust 5 0.755 0.863 0.906 0.1349 0.858 0.586
#> MAD:mclust 5 0.625 0.779 0.835 0.1118 0.865 0.613
#> ATC:mclust 5 0.790 0.823 0.896 0.0334 0.900 0.688
#> SD:kmeans 5 0.689 0.765 0.781 0.0797 0.778 0.434
#> CV:kmeans 5 0.614 0.541 0.699 0.0847 0.907 0.728
#> MAD:kmeans 5 0.697 0.791 0.829 0.0782 0.892 0.627
#> ATC:kmeans 5 0.677 0.667 0.801 0.0741 0.967 0.874
#> SD:pam 5 0.659 0.675 0.832 0.0560 0.924 0.809
#> CV:pam 5 0.525 0.647 0.797 0.0771 0.888 0.719
#> MAD:pam 5 0.520 0.609 0.743 0.0832 0.809 0.531
#> ATC:pam 5 0.755 0.819 0.906 0.2151 0.766 0.487
#> SD:hclust 5 0.436 0.650 0.754 0.1070 1.000 1.000
#> CV:hclust 5 0.404 0.677 0.750 0.0780 0.972 0.951
#> MAD:hclust 5 0.406 0.393 0.678 0.0846 0.683 0.430
#> ATC:hclust 5 0.466 0.717 0.842 0.1653 0.852 0.728
get_stats(res_list, k = 6)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> SD:NMF 6 0.604 0.555 0.726 0.0447 0.892 0.578
#> CV:NMF 6 0.604 0.539 0.732 0.0450 0.938 0.735
#> MAD:NMF 6 0.585 0.523 0.715 0.0466 0.881 0.540
#> ATC:NMF 6 0.561 0.603 0.761 0.0643 0.838 0.528
#> SD:skmeans 6 0.760 0.680 0.820 0.0365 0.990 0.949
#> CV:skmeans 6 0.683 0.606 0.774 0.0376 0.973 0.867
#> MAD:skmeans 6 0.716 0.624 0.786 0.0395 0.977 0.889
#> ATC:skmeans 6 0.765 0.647 0.779 0.0445 0.942 0.736
#> SD:mclust 6 0.707 0.683 0.802 0.0770 0.886 0.577
#> CV:mclust 6 0.716 0.754 0.846 0.0342 0.973 0.882
#> MAD:mclust 6 0.684 0.606 0.775 0.0576 0.932 0.732
#> ATC:mclust 6 0.737 0.787 0.865 0.0878 0.896 0.631
#> SD:kmeans 6 0.717 0.757 0.842 0.0570 0.987 0.939
#> CV:kmeans 6 0.701 0.729 0.788 0.0579 0.862 0.546
#> MAD:kmeans 6 0.703 0.729 0.809 0.0410 0.981 0.914
#> ATC:kmeans 6 0.697 0.618 0.769 0.0480 0.898 0.622
#> SD:pam 6 0.703 0.761 0.852 0.0363 0.984 0.952
#> CV:pam 6 0.598 0.561 0.780 0.0460 0.953 0.846
#> MAD:pam 6 0.548 0.609 0.744 0.0387 0.900 0.653
#> ATC:pam 6 0.784 0.820 0.892 0.0268 0.988 0.952
#> SD:hclust 6 0.422 0.563 0.700 0.0703 0.981 0.966
#> CV:hclust 6 0.396 0.673 0.713 0.0758 0.985 0.972
#> MAD:hclust 6 0.414 0.359 0.673 0.0380 0.940 0.854
#> ATC:hclust 6 0.464 0.616 0.787 0.0570 0.876 0.760
Following heatmap plots the partition for each combination of methods and the lightness correspond to the silhouette scores for samples in each method. On top the consensus subgroup is inferred from all methods by taking the mean silhouette scores as weight.
collect_stats(res_list, k = 2)
collect_stats(res_list, k = 3)
collect_stats(res_list, k = 4)
collect_stats(res_list, k = 5)
collect_stats(res_list, k = 6)
Collect partitions from all methods:
collect_classes(res_list, k = 2)
collect_classes(res_list, k = 3)
collect_classes(res_list, k = 4)
collect_classes(res_list, k = 5)
collect_classes(res_list, k = 6)
Overlap of top rows from different top-row methods:
top_rows_overlap(res_list, top_n = 1000, method = "euler")
top_rows_overlap(res_list, top_n = 2000, method = "euler")
top_rows_overlap(res_list, top_n = 3000, method = "euler")
top_rows_overlap(res_list, top_n = 4000, method = "euler")
top_rows_overlap(res_list, top_n = 5000, method = "euler")
Also visualize the correspondance of rankings between different top-row methods:
top_rows_overlap(res_list, top_n = 1000, method = "correspondance")
top_rows_overlap(res_list, top_n = 2000, method = "correspondance")
top_rows_overlap(res_list, top_n = 3000, method = "correspondance")
top_rows_overlap(res_list, top_n = 4000, method = "correspondance")
top_rows_overlap(res_list, top_n = 5000, method = "correspondance")
Heatmaps of the top rows:
top_rows_heatmap(res_list, top_n = 1000)
top_rows_heatmap(res_list, top_n = 2000)
top_rows_heatmap(res_list, top_n = 3000)
top_rows_heatmap(res_list, top_n = 4000)
top_rows_heatmap(res_list, top_n = 5000)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res_list, k = 2)
#> n tissue(p) k
#> SD:NMF 166 2.46e-15 2
#> CV:NMF 167 3.11e-15 2
#> MAD:NMF 169 3.59e-14 2
#> ATC:NMF 167 1.35e-18 2
#> SD:skmeans 169 1.87e-14 2
#> CV:skmeans 170 2.13e-14 2
#> MAD:skmeans 169 2.27e-14 2
#> ATC:skmeans 170 7.60e-15 2
#> SD:mclust 171 6.38e-29 2
#> CV:mclust 169 1.02e-30 2
#> MAD:mclust 169 1.38e-28 2
#> ATC:mclust 170 6.66e-31 2
#> SD:kmeans 171 4.03e-27 2
#> CV:kmeans 169 1.38e-28 2
#> MAD:kmeans 169 4.70e-26 2
#> ATC:kmeans 171 4.03e-27 2
#> SD:pam 170 3.24e-26 2
#> CV:pam 169 2.26e-28 2
#> MAD:pam 168 2.02e-26 2
#> ATC:pam 170 3.94e-28 2
#> SD:hclust 171 6.38e-29 2
#> CV:hclust 170 8.86e-30 2
#> MAD:hclust 142 4.59e-22 2
#> ATC:hclust 162 2.13e-27 2
test_to_known_factors(res_list, k = 3)
#> n tissue(p) k
#> SD:NMF 154 1.89e-17 3
#> CV:NMF 137 4.98e-14 3
#> MAD:NMF 137 1.39e-16 3
#> ATC:NMF 164 1.15e-24 3
#> SD:skmeans 159 4.62e-14 3
#> CV:skmeans 151 1.57e-14 3
#> MAD:skmeans 158 1.81e-13 3
#> ATC:skmeans 158 5.64e-20 3
#> SD:mclust 161 9.04e-32 3
#> CV:mclust 144 4.75e-29 3
#> MAD:mclust 165 8.50e-34 3
#> ATC:mclust 165 1.75e-33 3
#> SD:kmeans 167 3.00e-28 3
#> CV:kmeans 164 1.93e-27 3
#> MAD:kmeans 164 8.27e-29 3
#> ATC:kmeans 169 3.81e-29 3
#> SD:pam 161 2.90e-31 3
#> CV:pam 163 1.23e-30 3
#> MAD:pam 152 1.80e-29 3
#> ATC:pam 160 4.46e-28 3
#> SD:hclust 163 3.48e-32 3
#> CV:hclust 133 3.68e-23 3
#> MAD:hclust 138 4.21e-25 3
#> ATC:hclust 122 1.10e-18 3
test_to_known_factors(res_list, k = 4)
#> n tissue(p) k
#> SD:NMF 120 2.41e-15 4
#> CV:NMF 108 1.85e-16 4
#> MAD:NMF 126 3.40e-20 4
#> ATC:NMF 161 2.19e-25 4
#> SD:skmeans 162 2.36e-28 4
#> CV:skmeans 152 1.75e-21 4
#> MAD:skmeans 157 1.17e-26 4
#> ATC:skmeans 169 6.79e-27 4
#> SD:mclust 162 5.59e-33 4
#> CV:mclust 167 1.74e-33 4
#> MAD:mclust 164 9.74e-34 4
#> ATC:mclust 157 1.95e-29 4
#> SD:kmeans 48 5.27e-09 4
#> CV:kmeans 127 4.52e-26 4
#> MAD:kmeans 133 1.48e-24 4
#> ATC:kmeans 141 4.73e-27 4
#> SD:pam 164 1.78e-29 4
#> CV:pam 159 1.99e-30 4
#> MAD:pam 148 2.44e-30 4
#> ATC:pam 159 3.65e-28 4
#> SD:hclust 161 6.04e-36 4
#> CV:hclust 158 5.62e-29 4
#> MAD:hclust 116 1.38e-31 4
#> ATC:hclust 124 1.20e-19 4
test_to_known_factors(res_list, k = 5)
#> n tissue(p) k
#> SD:NMF 118 4.30e-23 5
#> CV:NMF 136 5.81e-26 5
#> MAD:NMF 104 1.48e-19 5
#> ATC:NMF 147 4.47e-22 5
#> SD:skmeans 156 2.71e-28 5
#> CV:skmeans 145 8.03e-24 5
#> MAD:skmeans 137 4.85e-25 5
#> ATC:skmeans 165 1.22e-23 5
#> SD:mclust 139 3.78e-27 5
#> CV:mclust 167 3.11e-33 5
#> MAD:mclust 159 1.53e-32 5
#> ATC:mclust 162 7.70e-30 5
#> SD:kmeans 160 2.75e-30 5
#> CV:kmeans 88 7.16e-23 5
#> MAD:kmeans 161 3.73e-32 5
#> ATC:kmeans 146 2.77e-25 5
#> SD:pam 130 2.82e-26 5
#> CV:pam 146 1.87e-27 5
#> MAD:pam 139 2.67e-25 5
#> ATC:pam 154 2.80e-29 5
#> SD:hclust 157 2.15e-34 5
#> CV:hclust 164 2.22e-30 5
#> MAD:hclust 83 2.78e-15 5
#> ATC:hclust 163 1.78e-30 5
test_to_known_factors(res_list, k = 6)
#> n tissue(p) k
#> SD:NMF 110 2.61e-21 6
#> CV:NMF 116 1.16e-23 6
#> MAD:NMF 102 2.51e-20 6
#> ATC:NMF 134 3.76e-22 6
#> SD:skmeans 140 3.78e-24 6
#> CV:skmeans 129 1.90e-22 6
#> MAD:skmeans 130 4.10e-24 6
#> ATC:skmeans 132 1.05e-19 6
#> SD:mclust 146 2.00e-29 6
#> CV:mclust 155 1.15e-30 6
#> MAD:mclust 137 8.29e-28 6
#> ATC:mclust 159 6.28e-30 6
#> SD:kmeans 151 5.91e-31 6
#> CV:kmeans 153 1.23e-30 6
#> MAD:kmeans 148 2.88e-32 6
#> ATC:kmeans 130 1.07e-24 6
#> SD:pam 159 2.21e-32 6
#> CV:pam 116 7.41e-24 6
#> MAD:pam 128 2.66e-22 6
#> ATC:pam 160 1.41e-30 6
#> SD:hclust 133 5.49e-28 6
#> CV:hclust 158 1.23e-27 6
#> MAD:hclust 73 9.16e-14 6
#> ATC:hclust 149 6.72e-29 6
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "hclust"]
# you can also extract it by
# res = res_list["SD:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.722 0.913 0.939 0.3442 0.701 0.701
#> 3 3 0.511 0.754 0.877 0.3351 0.894 0.849
#> 4 4 0.460 0.717 0.836 0.1500 0.961 0.934
#> 5 5 0.436 0.650 0.754 0.1070 1.000 1.000
#> 6 6 0.422 0.563 0.700 0.0703 0.981 0.966
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.1843 0.930 0.028 0.972
#> GSM152805 2 0.0938 0.929 0.012 0.988
#> GSM152806 2 0.0938 0.929 0.012 0.988
#> GSM152807 2 0.2236 0.928 0.036 0.964
#> GSM152808 2 0.0938 0.929 0.012 0.988
#> GSM152809 2 0.2236 0.928 0.036 0.964
#> GSM152810 2 0.6887 0.797 0.184 0.816
#> GSM152811 2 0.3733 0.898 0.072 0.928
#> GSM152812 2 0.2236 0.928 0.036 0.964
#> GSM152813 2 0.1843 0.931 0.028 0.972
#> GSM152814 2 0.1843 0.930 0.028 0.972
#> GSM152815 2 0.2423 0.927 0.040 0.960
#> GSM152816 2 0.0938 0.931 0.012 0.988
#> GSM152817 2 0.0938 0.929 0.012 0.988
#> GSM152818 2 0.0938 0.929 0.012 0.988
#> GSM152819 2 0.0938 0.929 0.012 0.988
#> GSM152820 2 0.4161 0.906 0.084 0.916
#> GSM152821 2 0.2043 0.930 0.032 0.968
#> GSM153115 2 0.7299 0.815 0.204 0.796
#> GSM153116 2 0.0938 0.929 0.012 0.988
#> GSM153117 2 0.0938 0.929 0.012 0.988
#> GSM153118 2 0.1184 0.932 0.016 0.984
#> GSM153119 2 0.0938 0.929 0.012 0.988
#> GSM153120 2 0.8813 0.695 0.300 0.700
#> GSM153121 2 0.0672 0.930 0.008 0.992
#> GSM153122 2 0.0938 0.929 0.012 0.988
#> GSM153123 2 0.0938 0.932 0.012 0.988
#> GSM153124 2 0.5629 0.876 0.132 0.868
#> GSM153125 2 0.7950 0.777 0.240 0.760
#> GSM153126 2 0.0938 0.929 0.012 0.988
#> GSM153127 2 0.2778 0.925 0.048 0.952
#> GSM153128 2 0.0672 0.930 0.008 0.992
#> GSM153129 2 0.1184 0.932 0.016 0.984
#> GSM153130 2 0.0938 0.929 0.012 0.988
#> GSM153131 2 0.0672 0.931 0.008 0.992
#> GSM153132 2 0.0672 0.930 0.008 0.992
#> GSM153133 2 0.0938 0.932 0.012 0.988
#> GSM153134 2 0.1633 0.931 0.024 0.976
#> GSM153135 2 0.2778 0.926 0.048 0.952
#> GSM153136 2 0.8207 0.757 0.256 0.744
#> GSM153137 2 0.3274 0.921 0.060 0.940
#> GSM153138 2 0.2603 0.927 0.044 0.956
#> GSM153139 2 0.0938 0.929 0.012 0.988
#> GSM153140 2 0.2603 0.929 0.044 0.956
#> GSM153141 2 0.2423 0.928 0.040 0.960
#> GSM153142 2 0.0938 0.929 0.012 0.988
#> GSM153143 2 0.2603 0.927 0.044 0.956
#> GSM153144 2 0.0376 0.931 0.004 0.996
#> GSM153145 2 0.0938 0.929 0.012 0.988
#> GSM153146 2 0.1184 0.932 0.016 0.984
#> GSM153147 2 0.0376 0.931 0.004 0.996
#> GSM153148 2 0.2778 0.925 0.048 0.952
#> GSM153149 2 0.1414 0.932 0.020 0.980
#> GSM153150 2 0.8267 0.753 0.260 0.740
#> GSM153151 2 0.0672 0.931 0.008 0.992
#> GSM153152 2 0.0376 0.931 0.004 0.996
#> GSM153153 2 0.1843 0.930 0.028 0.972
#> GSM153154 2 0.0672 0.930 0.008 0.992
#> GSM153155 2 0.1184 0.932 0.016 0.984
#> GSM153156 2 0.0672 0.930 0.008 0.992
#> GSM153157 2 0.0938 0.929 0.012 0.988
#> GSM153158 2 0.0938 0.929 0.012 0.988
#> GSM153159 2 0.0938 0.929 0.012 0.988
#> GSM153160 2 0.0938 0.929 0.012 0.988
#> GSM153161 2 0.3114 0.922 0.056 0.944
#> GSM153162 2 0.0376 0.931 0.004 0.996
#> GSM153163 2 0.0938 0.929 0.012 0.988
#> GSM153164 2 0.1184 0.930 0.016 0.984
#> GSM153165 2 0.0938 0.929 0.012 0.988
#> GSM153166 2 0.1633 0.931 0.024 0.976
#> GSM153167 2 0.1843 0.931 0.028 0.972
#> GSM153168 2 0.0938 0.929 0.012 0.988
#> GSM153169 2 0.0938 0.929 0.012 0.988
#> GSM153170 2 0.0938 0.929 0.012 0.988
#> GSM153171 2 0.6343 0.854 0.160 0.840
#> GSM153172 2 0.1414 0.931 0.020 0.980
#> GSM153173 2 0.0938 0.929 0.012 0.988
#> GSM153174 2 0.0376 0.931 0.004 0.996
#> GSM153175 2 0.7139 0.824 0.196 0.804
#> GSM153176 2 0.4562 0.899 0.096 0.904
#> GSM153177 2 0.1414 0.931 0.020 0.980
#> GSM152931 2 0.7883 0.781 0.236 0.764
#> GSM152932 2 0.2236 0.930 0.036 0.964
#> GSM152933 2 0.1184 0.932 0.016 0.984
#> GSM152934 2 0.4815 0.897 0.104 0.896
#> GSM152935 2 0.0672 0.930 0.008 0.992
#> GSM152936 2 0.6801 0.838 0.180 0.820
#> GSM152937 2 0.0672 0.930 0.008 0.992
#> GSM152938 2 0.0672 0.930 0.008 0.992
#> GSM152939 2 0.3114 0.922 0.056 0.944
#> GSM152940 2 0.8813 0.695 0.300 0.700
#> GSM152941 1 0.1843 0.978 0.972 0.028
#> GSM152942 2 0.1184 0.932 0.016 0.984
#> GSM152943 2 0.3114 0.923 0.056 0.944
#> GSM152944 2 0.0938 0.929 0.012 0.988
#> GSM152945 2 0.1184 0.932 0.016 0.984
#> GSM152946 2 0.3733 0.918 0.072 0.928
#> GSM152947 2 0.8081 0.769 0.248 0.752
#> GSM152948 2 0.2603 0.928 0.044 0.956
#> GSM152949 2 0.0376 0.931 0.004 0.996
#> GSM152950 2 0.0376 0.931 0.004 0.996
#> GSM152951 2 0.2236 0.930 0.036 0.964
#> GSM152952 2 0.2603 0.926 0.044 0.956
#> GSM152953 2 0.2778 0.926 0.048 0.952
#> GSM152954 2 0.8327 0.748 0.264 0.736
#> GSM152955 2 0.0376 0.930 0.004 0.996
#> GSM152956 2 0.2603 0.926 0.044 0.956
#> GSM152957 2 0.7056 0.827 0.192 0.808
#> GSM152958 2 0.8207 0.757 0.256 0.744
#> GSM152959 2 0.8267 0.753 0.260 0.740
#> GSM152960 2 0.7745 0.792 0.228 0.772
#> GSM152961 2 0.8909 0.682 0.308 0.692
#> GSM152962 2 0.0376 0.931 0.004 0.996
#> GSM152963 2 0.2778 0.925 0.048 0.952
#> GSM152964 2 0.1184 0.930 0.016 0.984
#> GSM152965 2 0.1184 0.932 0.016 0.984
#> GSM152966 2 0.7950 0.777 0.240 0.760
#> GSM152967 2 0.0672 0.931 0.008 0.992
#> GSM152968 2 0.0376 0.931 0.004 0.996
#> GSM152969 2 0.7950 0.777 0.240 0.760
#> GSM152970 2 0.6973 0.830 0.188 0.812
#> GSM152971 2 0.7950 0.777 0.240 0.760
#> GSM152972 2 0.8081 0.767 0.248 0.752
#> GSM152973 2 0.2948 0.924 0.052 0.948
#> GSM152974 2 0.1414 0.931 0.020 0.980
#> GSM152975 2 0.3879 0.912 0.076 0.924
#> GSM152976 2 0.6148 0.860 0.152 0.848
#> GSM152977 2 0.6438 0.849 0.164 0.836
#> GSM152978 2 0.8386 0.742 0.268 0.732
#> GSM152979 2 0.0938 0.929 0.012 0.988
#> GSM152980 2 0.4562 0.900 0.096 0.904
#> GSM152981 2 0.0938 0.929 0.012 0.988
#> GSM152982 2 0.6623 0.843 0.172 0.828
#> GSM152983 2 0.7528 0.803 0.216 0.784
#> GSM152984 2 0.2236 0.929 0.036 0.964
#> GSM152985 2 0.8861 0.689 0.304 0.696
#> GSM152986 2 0.7950 0.777 0.240 0.760
#> GSM152987 1 0.1414 0.989 0.980 0.020
#> GSM152988 2 0.2948 0.927 0.052 0.948
#> GSM152989 2 0.7299 0.816 0.204 0.796
#> GSM152990 2 0.0938 0.929 0.012 0.988
#> GSM152991 2 0.0938 0.929 0.012 0.988
#> GSM187524 1 0.0672 0.996 0.992 0.008
#> GSM187525 1 0.0672 0.996 0.992 0.008
#> GSM187526 1 0.0672 0.996 0.992 0.008
#> GSM187527 1 0.1633 0.983 0.976 0.024
#> GSM152856 1 0.0672 0.996 0.992 0.008
#> GSM152857 1 0.1414 0.987 0.980 0.020
#> GSM152858 1 0.0672 0.996 0.992 0.008
#> GSM152859 1 0.2423 0.968 0.960 0.040
#> GSM152860 1 0.0672 0.996 0.992 0.008
#> GSM152861 1 0.0672 0.996 0.992 0.008
#> GSM152862 1 0.0672 0.996 0.992 0.008
#> GSM152863 1 0.1184 0.991 0.984 0.016
#> GSM152864 1 0.0672 0.996 0.992 0.008
#> GSM152865 1 0.0672 0.996 0.992 0.008
#> GSM152866 1 0.0672 0.996 0.992 0.008
#> GSM152867 1 0.0672 0.996 0.992 0.008
#> GSM152868 1 0.0672 0.996 0.992 0.008
#> GSM152869 1 0.0672 0.996 0.992 0.008
#> GSM152870 1 0.0672 0.996 0.992 0.008
#> GSM152871 1 0.0672 0.996 0.992 0.008
#> GSM152872 1 0.0672 0.996 0.992 0.008
#> GSM152873 1 0.0672 0.996 0.992 0.008
#> GSM152874 1 0.0672 0.996 0.992 0.008
#> GSM152875 1 0.0672 0.996 0.992 0.008
#> GSM152876 1 0.0938 0.993 0.988 0.012
#> GSM152877 1 0.0672 0.996 0.992 0.008
#> GSM152878 1 0.0672 0.996 0.992 0.008
#> GSM152879 1 0.0672 0.996 0.992 0.008
#> GSM152880 1 0.0672 0.996 0.992 0.008
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.0747 0.807 0.000 0.984 0.016
#> GSM152805 3 0.6045 0.925 0.000 0.380 0.620
#> GSM152806 3 0.6045 0.925 0.000 0.380 0.620
#> GSM152807 2 0.0424 0.806 0.000 0.992 0.008
#> GSM152808 3 0.6045 0.925 0.000 0.380 0.620
#> GSM152809 2 0.0424 0.806 0.000 0.992 0.008
#> GSM152810 3 0.4291 0.660 0.000 0.180 0.820
#> GSM152811 3 0.5497 0.819 0.000 0.292 0.708
#> GSM152812 2 0.0424 0.806 0.000 0.992 0.008
#> GSM152813 2 0.0592 0.806 0.000 0.988 0.012
#> GSM152814 2 0.0424 0.806 0.000 0.992 0.008
#> GSM152815 2 0.0424 0.805 0.000 0.992 0.008
#> GSM152816 2 0.5016 0.496 0.000 0.760 0.240
#> GSM152817 3 0.6045 0.925 0.000 0.380 0.620
#> GSM152818 3 0.6045 0.925 0.000 0.380 0.620
#> GSM152819 2 0.5397 0.363 0.000 0.720 0.280
#> GSM152820 2 0.3237 0.793 0.032 0.912 0.056
#> GSM152821 2 0.0592 0.807 0.000 0.988 0.012
#> GSM153115 2 0.5263 0.696 0.088 0.828 0.084
#> GSM153116 2 0.6180 -0.338 0.000 0.584 0.416
#> GSM153117 2 0.4842 0.556 0.000 0.776 0.224
#> GSM153118 2 0.1411 0.803 0.000 0.964 0.036
#> GSM153119 2 0.6308 -0.630 0.000 0.508 0.492
#> GSM153120 2 0.6979 0.565 0.140 0.732 0.128
#> GSM153121 2 0.3340 0.746 0.000 0.880 0.120
#> GSM153122 3 0.6045 0.925 0.000 0.380 0.620
#> GSM153123 2 0.2066 0.795 0.000 0.940 0.060
#> GSM153124 2 0.3683 0.762 0.044 0.896 0.060
#> GSM153125 2 0.5965 0.656 0.100 0.792 0.108
#> GSM153126 2 0.4062 0.688 0.000 0.836 0.164
#> GSM153127 2 0.0747 0.804 0.000 0.984 0.016
#> GSM153128 2 0.3551 0.730 0.000 0.868 0.132
#> GSM153129 2 0.2261 0.794 0.000 0.932 0.068
#> GSM153130 2 0.4399 0.650 0.000 0.812 0.188
#> GSM153131 2 0.2356 0.790 0.000 0.928 0.072
#> GSM153132 2 0.2959 0.769 0.000 0.900 0.100
#> GSM153133 2 0.1753 0.798 0.000 0.952 0.048
#> GSM153134 2 0.1163 0.806 0.000 0.972 0.028
#> GSM153135 2 0.0829 0.805 0.004 0.984 0.012
#> GSM153136 2 0.6254 0.636 0.108 0.776 0.116
#> GSM153137 2 0.1163 0.801 0.000 0.972 0.028
#> GSM153138 2 0.0747 0.806 0.000 0.984 0.016
#> GSM153139 2 0.4399 0.650 0.000 0.812 0.188
#> GSM153140 2 0.1031 0.809 0.000 0.976 0.024
#> GSM153141 2 0.0475 0.806 0.004 0.992 0.004
#> GSM153142 3 0.6309 0.640 0.000 0.496 0.504
#> GSM153143 2 0.1129 0.808 0.004 0.976 0.020
#> GSM153144 2 0.2066 0.794 0.000 0.940 0.060
#> GSM153145 3 0.6045 0.925 0.000 0.380 0.620
#> GSM153146 2 0.1163 0.804 0.000 0.972 0.028
#> GSM153147 2 0.2537 0.781 0.000 0.920 0.080
#> GSM153148 2 0.0747 0.804 0.000 0.984 0.016
#> GSM153149 2 0.1163 0.805 0.000 0.972 0.028
#> GSM153150 2 0.6325 0.631 0.112 0.772 0.116
#> GSM153151 2 0.2448 0.790 0.000 0.924 0.076
#> GSM153152 2 0.1964 0.794 0.000 0.944 0.056
#> GSM153153 2 0.0892 0.808 0.000 0.980 0.020
#> GSM153154 2 0.2878 0.772 0.000 0.904 0.096
#> GSM153155 2 0.1289 0.803 0.000 0.968 0.032
#> GSM153156 2 0.3482 0.737 0.000 0.872 0.128
#> GSM153157 2 0.6180 -0.316 0.000 0.584 0.416
#> GSM153158 2 0.5560 0.292 0.000 0.700 0.300
#> GSM153159 2 0.6309 -0.648 0.000 0.504 0.496
#> GSM153160 2 0.4062 0.688 0.000 0.836 0.164
#> GSM153161 2 0.1031 0.802 0.000 0.976 0.024
#> GSM153162 2 0.2165 0.791 0.000 0.936 0.064
#> GSM153163 2 0.4399 0.650 0.000 0.812 0.188
#> GSM153164 2 0.4796 0.562 0.000 0.780 0.220
#> GSM153165 2 0.4346 0.655 0.000 0.816 0.184
#> GSM153166 2 0.1163 0.807 0.000 0.972 0.028
#> GSM153167 2 0.1031 0.807 0.000 0.976 0.024
#> GSM153168 3 0.6045 0.925 0.000 0.380 0.620
#> GSM153169 2 0.4452 0.642 0.000 0.808 0.192
#> GSM153170 2 0.4399 0.648 0.000 0.812 0.188
#> GSM153171 2 0.4384 0.740 0.064 0.868 0.068
#> GSM153172 2 0.0892 0.807 0.000 0.980 0.020
#> GSM153173 2 0.4399 0.650 0.000 0.812 0.188
#> GSM153174 2 0.2165 0.791 0.000 0.936 0.064
#> GSM153175 2 0.5093 0.703 0.076 0.836 0.088
#> GSM153176 2 0.3742 0.783 0.036 0.892 0.072
#> GSM153177 2 0.2448 0.788 0.000 0.924 0.076
#> GSM152931 2 0.5889 0.660 0.096 0.796 0.108
#> GSM152932 2 0.1267 0.808 0.004 0.972 0.024
#> GSM152933 2 0.1289 0.803 0.000 0.968 0.032
#> GSM152934 2 0.3375 0.784 0.044 0.908 0.048
#> GSM152935 2 0.2959 0.767 0.000 0.900 0.100
#> GSM152936 2 0.4836 0.722 0.080 0.848 0.072
#> GSM152937 2 0.3551 0.730 0.000 0.868 0.132
#> GSM152938 2 0.3551 0.730 0.000 0.868 0.132
#> GSM152939 2 0.2280 0.807 0.008 0.940 0.052
#> GSM152940 2 0.6979 0.565 0.140 0.732 0.128
#> GSM152941 1 0.2176 0.950 0.948 0.020 0.032
#> GSM152942 2 0.3267 0.757 0.000 0.884 0.116
#> GSM152943 2 0.1129 0.803 0.004 0.976 0.020
#> GSM152944 2 0.4291 0.665 0.000 0.820 0.180
#> GSM152945 2 0.1753 0.805 0.000 0.952 0.048
#> GSM152946 2 0.2313 0.805 0.024 0.944 0.032
#> GSM152947 2 0.6111 0.645 0.112 0.784 0.104
#> GSM152948 2 0.1267 0.808 0.004 0.972 0.024
#> GSM152949 2 0.2165 0.792 0.000 0.936 0.064
#> GSM152950 2 0.2261 0.791 0.000 0.932 0.068
#> GSM152951 2 0.0892 0.809 0.000 0.980 0.020
#> GSM152952 2 0.0592 0.804 0.000 0.988 0.012
#> GSM152953 2 0.0829 0.805 0.004 0.984 0.012
#> GSM152954 2 0.6394 0.625 0.116 0.768 0.116
#> GSM152955 2 0.2537 0.785 0.000 0.920 0.080
#> GSM152956 2 0.0592 0.804 0.000 0.988 0.012
#> GSM152957 2 0.5004 0.709 0.072 0.840 0.088
#> GSM152958 2 0.6254 0.636 0.108 0.776 0.116
#> GSM152959 2 0.6325 0.631 0.112 0.772 0.116
#> GSM152960 2 0.5731 0.672 0.088 0.804 0.108
#> GSM152961 2 0.7097 0.551 0.148 0.724 0.128
#> GSM152962 2 0.2448 0.784 0.000 0.924 0.076
#> GSM152963 2 0.0747 0.804 0.000 0.984 0.016
#> GSM152964 2 0.5465 0.331 0.000 0.712 0.288
#> GSM152965 2 0.1647 0.806 0.004 0.960 0.036
#> GSM152966 2 0.5965 0.656 0.100 0.792 0.108
#> GSM152967 2 0.1860 0.798 0.000 0.948 0.052
#> GSM152968 2 0.2261 0.789 0.000 0.932 0.068
#> GSM152969 2 0.5965 0.656 0.100 0.792 0.108
#> GSM152970 2 0.4925 0.712 0.080 0.844 0.076
#> GSM152971 2 0.5965 0.656 0.100 0.792 0.108
#> GSM152972 2 0.6111 0.647 0.104 0.784 0.112
#> GSM152973 2 0.2774 0.800 0.008 0.920 0.072
#> GSM152974 2 0.0892 0.807 0.000 0.980 0.020
#> GSM152975 2 0.3141 0.796 0.020 0.912 0.068
#> GSM152976 2 0.4458 0.744 0.056 0.864 0.080
#> GSM152977 2 0.5075 0.729 0.068 0.836 0.096
#> GSM152978 2 0.6462 0.619 0.116 0.764 0.120
#> GSM152979 2 0.4346 0.655 0.000 0.816 0.184
#> GSM152980 2 0.3253 0.785 0.036 0.912 0.052
#> GSM152981 3 0.6045 0.925 0.000 0.380 0.620
#> GSM152982 2 0.5012 0.725 0.080 0.840 0.080
#> GSM152983 2 0.5505 0.683 0.088 0.816 0.096
#> GSM152984 2 0.2384 0.805 0.008 0.936 0.056
#> GSM152985 2 0.7039 0.558 0.144 0.728 0.128
#> GSM152986 2 0.5965 0.656 0.100 0.792 0.108
#> GSM152987 1 0.4748 0.848 0.832 0.024 0.144
#> GSM152988 2 0.2280 0.810 0.008 0.940 0.052
#> GSM152989 2 0.5263 0.697 0.084 0.828 0.088
#> GSM152990 2 0.4346 0.655 0.000 0.816 0.184
#> GSM152991 2 0.4702 0.580 0.000 0.788 0.212
#> GSM187524 1 0.1163 0.970 0.972 0.000 0.028
#> GSM187525 1 0.1163 0.970 0.972 0.000 0.028
#> GSM187526 1 0.1163 0.970 0.972 0.000 0.028
#> GSM187527 1 0.1337 0.966 0.972 0.016 0.012
#> GSM152856 1 0.0592 0.979 0.988 0.000 0.012
#> GSM152857 1 0.1182 0.970 0.976 0.012 0.012
#> GSM152858 1 0.0237 0.979 0.996 0.000 0.004
#> GSM152859 1 0.5115 0.818 0.768 0.004 0.228
#> GSM152860 1 0.0237 0.979 0.996 0.000 0.004
#> GSM152861 1 0.0000 0.980 1.000 0.000 0.000
#> GSM152862 1 0.0237 0.979 0.996 0.000 0.004
#> GSM152863 1 0.0661 0.976 0.988 0.008 0.004
#> GSM152864 1 0.0000 0.980 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.980 1.000 0.000 0.000
#> GSM152866 1 0.0592 0.979 0.988 0.000 0.012
#> GSM152867 1 0.0000 0.980 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.980 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.980 1.000 0.000 0.000
#> GSM152870 1 0.0237 0.979 0.996 0.000 0.004
#> GSM152871 1 0.0237 0.979 0.996 0.000 0.004
#> GSM152872 1 0.0237 0.979 0.996 0.000 0.004
#> GSM152873 1 0.0592 0.979 0.988 0.000 0.012
#> GSM152874 1 0.0592 0.979 0.988 0.000 0.012
#> GSM152875 1 0.0592 0.979 0.988 0.000 0.012
#> GSM152876 1 0.0829 0.977 0.984 0.004 0.012
#> GSM152877 1 0.0592 0.979 0.988 0.000 0.012
#> GSM152878 1 0.0592 0.979 0.988 0.000 0.012
#> GSM152879 1 0.0592 0.979 0.988 0.000 0.012
#> GSM152880 1 0.0592 0.979 0.988 0.000 0.012
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.0804 0.82900 0.000 0.980 0.012 0.008
#> GSM152805 3 0.2675 0.83247 0.000 0.100 0.892 0.008
#> GSM152806 3 0.2675 0.83247 0.000 0.100 0.892 0.008
#> GSM152807 2 0.0524 0.82772 0.000 0.988 0.004 0.008
#> GSM152808 3 0.2675 0.83247 0.000 0.100 0.892 0.008
#> GSM152809 2 0.0524 0.82772 0.000 0.988 0.004 0.008
#> GSM152810 3 0.3157 0.51698 0.000 0.004 0.852 0.144
#> GSM152811 3 0.3542 0.71511 0.000 0.060 0.864 0.076
#> GSM152812 2 0.0524 0.82772 0.000 0.988 0.004 0.008
#> GSM152813 2 0.1022 0.82948 0.000 0.968 0.032 0.000
#> GSM152814 2 0.0469 0.82881 0.000 0.988 0.012 0.000
#> GSM152815 2 0.0592 0.82620 0.000 0.984 0.000 0.016
#> GSM152816 2 0.5016 0.31306 0.000 0.600 0.396 0.004
#> GSM152817 3 0.2675 0.83247 0.000 0.100 0.892 0.008
#> GSM152818 3 0.2675 0.83247 0.000 0.100 0.892 0.008
#> GSM152819 2 0.4972 0.12008 0.000 0.544 0.456 0.000
#> GSM152820 2 0.2797 0.82526 0.000 0.900 0.032 0.068
#> GSM152821 2 0.0895 0.82961 0.000 0.976 0.020 0.004
#> GSM153115 2 0.3626 0.75135 0.004 0.812 0.000 0.184
#> GSM153116 3 0.4837 0.56857 0.000 0.348 0.648 0.004
#> GSM153117 2 0.4564 0.53480 0.000 0.672 0.328 0.000
#> GSM153118 2 0.1211 0.82837 0.000 0.960 0.040 0.000
#> GSM153119 3 0.4220 0.71703 0.000 0.248 0.748 0.004
#> GSM153120 2 0.4663 0.66422 0.012 0.716 0.000 0.272
#> GSM153121 2 0.3649 0.73411 0.000 0.796 0.204 0.000
#> GSM153122 3 0.2675 0.82922 0.000 0.100 0.892 0.008
#> GSM153123 2 0.2281 0.81218 0.000 0.904 0.096 0.000
#> GSM153124 2 0.2983 0.80093 0.004 0.880 0.008 0.108
#> GSM153125 2 0.3982 0.72526 0.004 0.776 0.000 0.220
#> GSM153126 2 0.4422 0.66544 0.000 0.736 0.256 0.008
#> GSM153127 2 0.0817 0.82563 0.000 0.976 0.000 0.024
#> GSM153128 2 0.3972 0.72670 0.000 0.788 0.204 0.008
#> GSM153129 2 0.2469 0.81118 0.000 0.892 0.108 0.000
#> GSM153130 2 0.4621 0.62178 0.000 0.708 0.284 0.008
#> GSM153131 2 0.2773 0.80150 0.000 0.880 0.116 0.004
#> GSM153132 2 0.3311 0.77100 0.000 0.828 0.172 0.000
#> GSM153133 2 0.1978 0.82329 0.000 0.928 0.068 0.004
#> GSM153134 2 0.1637 0.82554 0.000 0.940 0.060 0.000
#> GSM153135 2 0.0817 0.82610 0.000 0.976 0.000 0.024
#> GSM153136 2 0.4122 0.71135 0.004 0.760 0.000 0.236
#> GSM153137 2 0.1118 0.82372 0.000 0.964 0.000 0.036
#> GSM153138 2 0.0779 0.82818 0.000 0.980 0.004 0.016
#> GSM153139 2 0.4621 0.62178 0.000 0.708 0.284 0.008
#> GSM153140 2 0.1798 0.83352 0.000 0.944 0.040 0.016
#> GSM153141 2 0.0592 0.82672 0.000 0.984 0.000 0.016
#> GSM153142 3 0.3907 0.73596 0.000 0.232 0.768 0.000
#> GSM153143 2 0.1114 0.82948 0.004 0.972 0.008 0.016
#> GSM153144 2 0.2530 0.81122 0.000 0.896 0.100 0.004
#> GSM153145 3 0.2675 0.83247 0.000 0.100 0.892 0.008
#> GSM153146 2 0.1305 0.82876 0.000 0.960 0.036 0.004
#> GSM153147 2 0.2888 0.79896 0.000 0.872 0.124 0.004
#> GSM153148 2 0.0817 0.82563 0.000 0.976 0.000 0.024
#> GSM153149 2 0.1489 0.82840 0.000 0.952 0.044 0.004
#> GSM153150 2 0.4155 0.70888 0.004 0.756 0.000 0.240
#> GSM153151 2 0.2976 0.80150 0.000 0.872 0.120 0.008
#> GSM153152 2 0.2408 0.80801 0.000 0.896 0.104 0.000
#> GSM153153 2 0.1398 0.83128 0.000 0.956 0.040 0.004
#> GSM153154 2 0.3266 0.77482 0.000 0.832 0.168 0.000
#> GSM153155 2 0.1211 0.82708 0.000 0.960 0.040 0.000
#> GSM153156 2 0.3688 0.72950 0.000 0.792 0.208 0.000
#> GSM153157 3 0.5007 0.53545 0.000 0.356 0.636 0.008
#> GSM153158 2 0.4994 0.03033 0.000 0.520 0.480 0.000
#> GSM153159 3 0.4164 0.70157 0.000 0.264 0.736 0.000
#> GSM153160 2 0.4422 0.66544 0.000 0.736 0.256 0.008
#> GSM153161 2 0.1022 0.82469 0.000 0.968 0.000 0.032
#> GSM153162 2 0.2654 0.80773 0.000 0.888 0.108 0.004
#> GSM153163 2 0.4621 0.62178 0.000 0.708 0.284 0.008
#> GSM153164 2 0.4543 0.53998 0.000 0.676 0.324 0.000
#> GSM153165 2 0.4594 0.62624 0.000 0.712 0.280 0.008
#> GSM153166 2 0.1637 0.82634 0.000 0.940 0.060 0.000
#> GSM153167 2 0.1557 0.82655 0.000 0.944 0.056 0.000
#> GSM153168 3 0.2675 0.83247 0.000 0.100 0.892 0.008
#> GSM153169 2 0.4647 0.61473 0.000 0.704 0.288 0.008
#> GSM153170 2 0.4567 0.63429 0.000 0.716 0.276 0.008
#> GSM153171 2 0.3289 0.78207 0.004 0.852 0.004 0.140
#> GSM153172 2 0.1022 0.82946 0.000 0.968 0.032 0.000
#> GSM153173 2 0.4621 0.62178 0.000 0.708 0.284 0.008
#> GSM153174 2 0.2593 0.80894 0.000 0.892 0.104 0.004
#> GSM153175 2 0.3721 0.75713 0.004 0.816 0.004 0.176
#> GSM153176 2 0.3689 0.81607 0.004 0.860 0.048 0.088
#> GSM153177 2 0.2921 0.79098 0.000 0.860 0.140 0.000
#> GSM152931 2 0.3945 0.72854 0.004 0.780 0.000 0.216
#> GSM152932 2 0.1356 0.83192 0.000 0.960 0.032 0.008
#> GSM152933 2 0.1211 0.82708 0.000 0.960 0.040 0.000
#> GSM152934 2 0.2742 0.82143 0.000 0.900 0.024 0.076
#> GSM152935 2 0.3052 0.79060 0.000 0.860 0.136 0.004
#> GSM152936 2 0.3441 0.77675 0.004 0.840 0.004 0.152
#> GSM152937 2 0.3893 0.73190 0.000 0.796 0.196 0.008
#> GSM152938 2 0.3893 0.73190 0.000 0.796 0.196 0.008
#> GSM152939 2 0.2317 0.83154 0.004 0.928 0.036 0.032
#> GSM152940 2 0.4663 0.66422 0.012 0.716 0.000 0.272
#> GSM152941 1 0.4882 0.24691 0.708 0.020 0.000 0.272
#> GSM152942 2 0.3978 0.74771 0.000 0.796 0.192 0.012
#> GSM152943 2 0.1356 0.82751 0.000 0.960 0.008 0.032
#> GSM152944 2 0.4511 0.65054 0.000 0.724 0.268 0.008
#> GSM152945 2 0.2174 0.83036 0.000 0.928 0.052 0.020
#> GSM152946 2 0.2111 0.83147 0.000 0.932 0.024 0.044
#> GSM152947 2 0.4158 0.72065 0.008 0.768 0.000 0.224
#> GSM152948 2 0.1297 0.83227 0.000 0.964 0.016 0.020
#> GSM152949 2 0.2589 0.80347 0.000 0.884 0.116 0.000
#> GSM152950 2 0.2704 0.80304 0.000 0.876 0.124 0.000
#> GSM152951 2 0.1059 0.83182 0.000 0.972 0.016 0.012
#> GSM152952 2 0.0707 0.82548 0.000 0.980 0.000 0.020
#> GSM152953 2 0.0817 0.82572 0.000 0.976 0.000 0.024
#> GSM152954 2 0.4188 0.70416 0.004 0.752 0.000 0.244
#> GSM152955 2 0.2859 0.80838 0.000 0.880 0.112 0.008
#> GSM152956 2 0.0707 0.82548 0.000 0.980 0.000 0.020
#> GSM152957 2 0.3494 0.76149 0.004 0.824 0.000 0.172
#> GSM152958 2 0.4122 0.71135 0.004 0.760 0.000 0.236
#> GSM152959 2 0.4155 0.70809 0.004 0.756 0.000 0.240
#> GSM152960 2 0.3870 0.73779 0.004 0.788 0.000 0.208
#> GSM152961 2 0.4804 0.65412 0.016 0.708 0.000 0.276
#> GSM152962 2 0.2831 0.79823 0.000 0.876 0.120 0.004
#> GSM152963 2 0.0817 0.82517 0.000 0.976 0.000 0.024
#> GSM152964 2 0.5165 -0.00508 0.000 0.512 0.484 0.004
#> GSM152965 2 0.2048 0.82752 0.000 0.928 0.064 0.008
#> GSM152966 2 0.3982 0.72526 0.004 0.776 0.000 0.220
#> GSM152967 2 0.2149 0.81679 0.000 0.912 0.088 0.000
#> GSM152968 2 0.2704 0.79915 0.000 0.876 0.124 0.000
#> GSM152969 2 0.3982 0.72526 0.004 0.776 0.000 0.220
#> GSM152970 2 0.3545 0.76328 0.008 0.828 0.000 0.164
#> GSM152971 2 0.3982 0.72526 0.004 0.776 0.000 0.220
#> GSM152972 2 0.4053 0.71897 0.004 0.768 0.000 0.228
#> GSM152973 2 0.3100 0.82359 0.004 0.888 0.080 0.028
#> GSM152974 2 0.1118 0.83035 0.000 0.964 0.036 0.000
#> GSM152975 2 0.3029 0.82689 0.004 0.896 0.048 0.052
#> GSM152976 2 0.3432 0.78610 0.004 0.848 0.008 0.140
#> GSM152977 2 0.4093 0.77898 0.004 0.816 0.024 0.156
#> GSM152978 2 0.4220 0.70007 0.004 0.748 0.000 0.248
#> GSM152979 2 0.4511 0.64584 0.000 0.724 0.268 0.008
#> GSM152980 2 0.2742 0.82053 0.000 0.900 0.024 0.076
#> GSM152981 3 0.2675 0.83247 0.000 0.100 0.892 0.008
#> GSM152982 2 0.3988 0.77657 0.004 0.820 0.020 0.156
#> GSM152983 2 0.3751 0.74508 0.004 0.800 0.000 0.196
#> GSM152984 2 0.2549 0.83072 0.004 0.916 0.056 0.024
#> GSM152985 2 0.4690 0.65929 0.012 0.712 0.000 0.276
#> GSM152986 2 0.3982 0.72508 0.004 0.776 0.000 0.220
#> GSM152987 4 0.4978 0.00000 0.384 0.004 0.000 0.612
#> GSM152988 2 0.2699 0.83015 0.000 0.904 0.068 0.028
#> GSM152989 2 0.3626 0.75298 0.004 0.812 0.000 0.184
#> GSM152990 2 0.4511 0.64565 0.000 0.724 0.268 0.008
#> GSM152991 2 0.4741 0.51853 0.000 0.668 0.328 0.004
#> GSM187524 1 0.3942 0.42122 0.764 0.000 0.000 0.236
#> GSM187525 1 0.4008 0.42144 0.756 0.000 0.000 0.244
#> GSM187526 1 0.3764 0.44980 0.784 0.000 0.000 0.216
#> GSM187527 1 0.4632 0.60611 0.740 0.012 0.004 0.244
#> GSM152856 1 0.4155 0.63905 0.756 0.000 0.004 0.240
#> GSM152857 1 0.4600 0.61382 0.744 0.012 0.004 0.240
#> GSM152858 1 0.1716 0.66885 0.936 0.000 0.000 0.064
#> GSM152859 1 0.6074 0.12578 0.648 0.000 0.084 0.268
#> GSM152860 1 0.1716 0.66885 0.936 0.000 0.000 0.064
#> GSM152861 1 0.0817 0.69198 0.976 0.000 0.000 0.024
#> GSM152862 1 0.1716 0.66885 0.936 0.000 0.000 0.064
#> GSM152863 1 0.2922 0.67639 0.884 0.008 0.004 0.104
#> GSM152864 1 0.0817 0.69198 0.976 0.000 0.000 0.024
#> GSM152865 1 0.0817 0.69198 0.976 0.000 0.000 0.024
#> GSM152866 1 0.4188 0.63616 0.752 0.000 0.004 0.244
#> GSM152867 1 0.0817 0.69198 0.976 0.000 0.000 0.024
#> GSM152868 1 0.0817 0.69198 0.976 0.000 0.000 0.024
#> GSM152869 1 0.0817 0.69198 0.976 0.000 0.000 0.024
#> GSM152870 1 0.1716 0.66885 0.936 0.000 0.000 0.064
#> GSM152871 1 0.1716 0.66885 0.936 0.000 0.000 0.064
#> GSM152872 1 0.1716 0.66885 0.936 0.000 0.000 0.064
#> GSM152873 1 0.4155 0.63905 0.756 0.000 0.004 0.240
#> GSM152874 1 0.4155 0.63905 0.756 0.000 0.004 0.240
#> GSM152875 1 0.4155 0.63905 0.756 0.000 0.004 0.240
#> GSM152876 1 0.4335 0.63134 0.752 0.004 0.004 0.240
#> GSM152877 1 0.4155 0.63905 0.756 0.000 0.004 0.240
#> GSM152878 1 0.4155 0.63905 0.756 0.000 0.004 0.240
#> GSM152879 1 0.4155 0.63905 0.756 0.000 0.004 0.240
#> GSM152880 1 0.4155 0.63905 0.756 0.000 0.004 0.240
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.0671 0.7789 0.000 0.980 NA 0.016 0.004
#> GSM152805 5 0.0794 0.7776 0.000 0.028 NA 0.000 0.972
#> GSM152806 5 0.0609 0.7771 0.000 0.020 NA 0.000 0.980
#> GSM152807 2 0.0671 0.7779 0.000 0.980 NA 0.016 0.004
#> GSM152808 5 0.0609 0.7771 0.000 0.020 NA 0.000 0.980
#> GSM152809 2 0.0671 0.7779 0.000 0.980 NA 0.016 0.004
#> GSM152810 5 0.4413 0.4384 0.000 0.000 NA 0.044 0.724
#> GSM152811 5 0.3548 0.6076 0.000 0.008 NA 0.044 0.836
#> GSM152812 2 0.0771 0.7780 0.000 0.976 NA 0.020 0.004
#> GSM152813 2 0.1195 0.7802 0.000 0.960 NA 0.012 0.028
#> GSM152814 2 0.0807 0.7789 0.000 0.976 NA 0.012 0.012
#> GSM152815 2 0.0794 0.7767 0.000 0.972 NA 0.028 0.000
#> GSM152816 2 0.5302 0.2374 0.000 0.536 NA 0.052 0.412
#> GSM152817 5 0.0609 0.7771 0.000 0.020 NA 0.000 0.980
#> GSM152818 5 0.0794 0.7776 0.000 0.028 NA 0.000 0.972
#> GSM152819 2 0.5399 0.1036 0.000 0.496 NA 0.056 0.448
#> GSM152820 2 0.2540 0.7803 0.000 0.888 NA 0.088 0.024
#> GSM152821 2 0.1117 0.7797 0.000 0.964 NA 0.016 0.020
#> GSM153115 2 0.3790 0.6656 0.000 0.724 NA 0.272 0.000
#> GSM153116 5 0.5179 0.4957 0.000 0.288 NA 0.072 0.640
#> GSM153117 2 0.5271 0.5178 0.000 0.628 NA 0.076 0.296
#> GSM153118 2 0.1493 0.7771 0.000 0.948 NA 0.028 0.024
#> GSM153119 5 0.4313 0.6396 0.000 0.172 NA 0.068 0.760
#> GSM153120 2 0.4126 0.5480 0.000 0.620 NA 0.380 0.000
#> GSM153121 2 0.5032 0.6377 0.000 0.704 NA 0.128 0.168
#> GSM153122 5 0.1117 0.7706 0.000 0.020 NA 0.016 0.964
#> GSM153123 2 0.2914 0.7569 0.000 0.872 NA 0.052 0.076
#> GSM153124 2 0.3209 0.7362 0.000 0.812 NA 0.180 0.008
#> GSM153125 2 0.3895 0.6203 0.000 0.680 NA 0.320 0.000
#> GSM153126 2 0.5680 0.5474 0.000 0.628 NA 0.160 0.212
#> GSM153127 2 0.1197 0.7749 0.000 0.952 NA 0.048 0.000
#> GSM153128 2 0.5159 0.6239 0.000 0.692 NA 0.164 0.144
#> GSM153129 2 0.3242 0.7583 0.000 0.852 NA 0.076 0.072
#> GSM153130 2 0.5810 0.5058 0.000 0.604 NA 0.152 0.244
#> GSM153131 2 0.3702 0.7347 0.000 0.820 NA 0.084 0.096
#> GSM153132 2 0.3995 0.7167 0.000 0.788 NA 0.060 0.152
#> GSM153133 2 0.2554 0.7693 0.000 0.892 NA 0.072 0.036
#> GSM153134 2 0.1965 0.7761 0.000 0.924 NA 0.024 0.052
#> GSM153135 2 0.1270 0.7754 0.000 0.948 NA 0.052 0.000
#> GSM153136 2 0.3983 0.5989 0.000 0.660 NA 0.340 0.000
#> GSM153137 2 0.1608 0.7725 0.000 0.928 NA 0.072 0.000
#> GSM153138 2 0.0865 0.7787 0.000 0.972 NA 0.024 0.004
#> GSM153139 2 0.5810 0.5058 0.000 0.604 NA 0.152 0.244
#> GSM153140 2 0.1997 0.7851 0.000 0.924 NA 0.040 0.036
#> GSM153141 2 0.0963 0.7768 0.000 0.964 NA 0.036 0.000
#> GSM153142 5 0.4125 0.6469 0.000 0.172 NA 0.056 0.772
#> GSM153143 2 0.1571 0.7793 0.000 0.936 NA 0.060 0.004
#> GSM153144 2 0.3464 0.7483 0.000 0.836 NA 0.096 0.068
#> GSM153145 5 0.0609 0.7771 0.000 0.020 NA 0.000 0.980
#> GSM153146 2 0.1399 0.7782 0.000 0.952 NA 0.028 0.020
#> GSM153147 2 0.3704 0.7358 0.000 0.820 NA 0.088 0.092
#> GSM153148 2 0.1197 0.7749 0.000 0.952 NA 0.048 0.000
#> GSM153149 2 0.1907 0.7785 0.000 0.928 NA 0.044 0.028
#> GSM153150 2 0.3999 0.5968 0.000 0.656 NA 0.344 0.000
#> GSM153151 2 0.3810 0.7331 0.000 0.812 NA 0.100 0.088
#> GSM153152 2 0.3301 0.7464 0.000 0.848 NA 0.080 0.072
#> GSM153153 2 0.1579 0.7806 0.000 0.944 NA 0.024 0.032
#> GSM153154 2 0.4179 0.7131 0.000 0.776 NA 0.072 0.152
#> GSM153155 2 0.1403 0.7765 0.000 0.952 NA 0.024 0.024
#> GSM153156 2 0.5115 0.6287 0.000 0.696 NA 0.136 0.168
#> GSM153157 5 0.5491 0.5047 0.000 0.276 NA 0.080 0.636
#> GSM153158 2 0.5694 0.0291 0.000 0.460 NA 0.080 0.460
#> GSM153159 5 0.4465 0.6035 0.000 0.204 NA 0.060 0.736
#> GSM153160 2 0.5680 0.5474 0.000 0.628 NA 0.160 0.212
#> GSM153161 2 0.1478 0.7743 0.000 0.936 NA 0.064 0.000
#> GSM153162 2 0.3586 0.7445 0.000 0.828 NA 0.096 0.076
#> GSM153163 2 0.5810 0.5058 0.000 0.604 NA 0.152 0.244
#> GSM153164 2 0.5252 0.5224 0.000 0.632 NA 0.076 0.292
#> GSM153165 2 0.5787 0.5107 0.000 0.608 NA 0.152 0.240
#> GSM153166 2 0.1872 0.7774 0.000 0.928 NA 0.020 0.052
#> GSM153167 2 0.1872 0.7769 0.000 0.928 NA 0.020 0.052
#> GSM153168 5 0.0771 0.7760 0.000 0.020 NA 0.004 0.976
#> GSM153169 2 0.5791 0.4976 0.000 0.600 NA 0.140 0.260
#> GSM153170 2 0.5764 0.5197 0.000 0.612 NA 0.152 0.236
#> GSM153171 2 0.3647 0.7010 0.000 0.764 NA 0.228 0.004
#> GSM153172 2 0.1661 0.7825 0.000 0.940 NA 0.036 0.024
#> GSM153173 2 0.5810 0.5058 0.000 0.604 NA 0.152 0.244
#> GSM153174 2 0.3526 0.7461 0.000 0.832 NA 0.096 0.072
#> GSM153175 2 0.3715 0.6832 0.000 0.736 NA 0.260 0.004
#> GSM153176 2 0.3885 0.7559 0.000 0.784 NA 0.176 0.040
#> GSM153177 2 0.3485 0.7373 0.000 0.828 NA 0.048 0.124
#> GSM152931 2 0.3895 0.6256 0.000 0.680 NA 0.320 0.000
#> GSM152932 2 0.1579 0.7816 0.000 0.944 NA 0.024 0.032
#> GSM152933 2 0.1403 0.7765 0.000 0.952 NA 0.024 0.024
#> GSM152934 2 0.3284 0.7696 0.000 0.828 NA 0.148 0.024
#> GSM152935 2 0.3702 0.7374 0.000 0.820 NA 0.084 0.096
#> GSM152936 2 0.3579 0.6942 0.000 0.756 NA 0.240 0.004
#> GSM152937 2 0.5079 0.6301 0.000 0.700 NA 0.164 0.136
#> GSM152938 2 0.5079 0.6301 0.000 0.700 NA 0.164 0.136
#> GSM152939 2 0.3141 0.7764 0.000 0.852 NA 0.108 0.040
#> GSM152940 2 0.4138 0.5399 0.000 0.616 NA 0.384 0.000
#> GSM152941 1 0.5884 0.1042 0.620 0.020 NA 0.092 0.000
#> GSM152942 2 0.4884 0.6731 0.000 0.720 NA 0.128 0.152
#> GSM152943 2 0.1671 0.7804 0.000 0.924 NA 0.076 0.000
#> GSM152944 2 0.5644 0.5469 0.000 0.628 NA 0.144 0.228
#> GSM152945 2 0.4074 0.7139 0.000 0.780 NA 0.180 0.012
#> GSM152946 2 0.2390 0.7819 0.000 0.896 NA 0.084 0.020
#> GSM152947 2 0.4101 0.6035 0.000 0.664 NA 0.332 0.000
#> GSM152948 2 0.1697 0.7833 0.000 0.932 NA 0.060 0.008
#> GSM152949 2 0.3536 0.7404 0.000 0.832 NA 0.084 0.084
#> GSM152950 2 0.3579 0.7424 0.000 0.828 NA 0.072 0.100
#> GSM152951 2 0.1408 0.7845 0.000 0.948 NA 0.044 0.008
#> GSM152952 2 0.1270 0.7746 0.000 0.948 NA 0.052 0.000
#> GSM152953 2 0.0880 0.7774 0.000 0.968 NA 0.032 0.000
#> GSM152954 2 0.4135 0.5960 0.000 0.656 NA 0.340 0.000
#> GSM152955 2 0.3359 0.7550 0.000 0.844 NA 0.084 0.072
#> GSM152956 2 0.1121 0.7750 0.000 0.956 NA 0.044 0.000
#> GSM152957 2 0.3586 0.6719 0.000 0.736 NA 0.264 0.000
#> GSM152958 2 0.3983 0.5989 0.000 0.660 NA 0.340 0.000
#> GSM152959 2 0.4118 0.6060 0.000 0.660 NA 0.336 0.000
#> GSM152960 2 0.3707 0.6610 0.000 0.716 NA 0.284 0.000
#> GSM152961 2 0.4438 0.5268 0.004 0.608 NA 0.384 0.000
#> GSM152962 2 0.3810 0.7275 0.000 0.812 NA 0.100 0.088
#> GSM152963 2 0.1197 0.7746 0.000 0.952 NA 0.048 0.000
#> GSM152964 2 0.6620 -0.0833 0.000 0.440 NA 0.108 0.424
#> GSM152965 2 0.2304 0.7776 0.000 0.908 NA 0.048 0.044
#> GSM152966 2 0.3895 0.6203 0.000 0.680 NA 0.320 0.000
#> GSM152967 2 0.2983 0.7605 0.000 0.868 NA 0.076 0.056
#> GSM152968 2 0.3754 0.7329 0.000 0.816 NA 0.084 0.100
#> GSM152969 2 0.3895 0.6203 0.000 0.680 NA 0.320 0.000
#> GSM152970 2 0.3895 0.6648 0.004 0.728 NA 0.264 0.000
#> GSM152971 2 0.3895 0.6203 0.000 0.680 NA 0.320 0.000
#> GSM152972 2 0.3932 0.6122 0.000 0.672 NA 0.328 0.000
#> GSM152973 2 0.3828 0.7635 0.000 0.808 NA 0.120 0.072
#> GSM152974 2 0.1818 0.7810 0.000 0.932 NA 0.044 0.024
#> GSM152975 2 0.3317 0.7685 0.000 0.840 NA 0.116 0.044
#> GSM152976 2 0.3582 0.7098 0.000 0.768 NA 0.224 0.008
#> GSM152977 2 0.4026 0.7025 0.000 0.736 NA 0.244 0.020
#> GSM152978 2 0.4166 0.5856 0.000 0.648 NA 0.348 0.000
#> GSM152979 2 0.5715 0.5323 0.000 0.620 NA 0.152 0.228
#> GSM152980 2 0.2616 0.7748 0.000 0.880 NA 0.100 0.020
#> GSM152981 5 0.0771 0.7760 0.000 0.020 NA 0.004 0.976
#> GSM152982 2 0.4080 0.6905 0.000 0.728 NA 0.252 0.020
#> GSM152983 2 0.3752 0.6486 0.000 0.708 NA 0.292 0.000
#> GSM152984 2 0.3437 0.7734 0.000 0.832 NA 0.120 0.048
#> GSM152985 2 0.4288 0.5336 0.000 0.612 NA 0.384 0.000
#> GSM152986 2 0.3895 0.6200 0.000 0.680 NA 0.320 0.000
#> GSM152987 4 0.6158 0.0000 0.204 0.004 NA 0.580 0.000
#> GSM152988 2 0.3569 0.7775 0.000 0.828 NA 0.104 0.068
#> GSM152989 2 0.3707 0.6544 0.000 0.716 NA 0.284 0.000
#> GSM152990 2 0.5618 0.5491 0.000 0.632 NA 0.144 0.224
#> GSM152991 2 0.5373 0.4810 0.000 0.620 NA 0.084 0.296
#> GSM187524 1 0.4218 0.2750 0.660 0.000 NA 0.008 0.000
#> GSM187525 1 0.4508 0.2610 0.648 0.000 NA 0.020 0.000
#> GSM187526 1 0.4360 0.2976 0.692 0.000 NA 0.024 0.000
#> GSM187527 1 0.4505 0.5990 0.620 0.008 NA 0.004 0.000
#> GSM152856 1 0.4088 0.6145 0.632 0.000 NA 0.000 0.000
#> GSM152857 1 0.4367 0.6012 0.620 0.008 NA 0.000 0.000
#> GSM152858 1 0.2362 0.6276 0.900 0.000 NA 0.024 0.000
#> GSM152859 1 0.5283 0.0143 0.540 0.000 NA 0.028 0.012
#> GSM152860 1 0.2362 0.6276 0.900 0.000 NA 0.024 0.000
#> GSM152861 1 0.0451 0.6526 0.988 0.000 NA 0.008 0.000
#> GSM152862 1 0.2362 0.6276 0.900 0.000 NA 0.024 0.000
#> GSM152863 1 0.2848 0.6482 0.840 0.004 NA 0.000 0.000
#> GSM152864 1 0.0451 0.6526 0.988 0.000 NA 0.008 0.000
#> GSM152865 1 0.0451 0.6526 0.988 0.000 NA 0.008 0.000
#> GSM152866 1 0.4088 0.6142 0.632 0.000 NA 0.000 0.000
#> GSM152867 1 0.0451 0.6526 0.988 0.000 NA 0.008 0.000
#> GSM152868 1 0.0451 0.6526 0.988 0.000 NA 0.008 0.000
#> GSM152869 1 0.0451 0.6526 0.988 0.000 NA 0.008 0.000
#> GSM152870 1 0.2362 0.6276 0.900 0.000 NA 0.024 0.000
#> GSM152871 1 0.2362 0.6276 0.900 0.000 NA 0.024 0.000
#> GSM152872 1 0.2362 0.6276 0.900 0.000 NA 0.024 0.000
#> GSM152873 1 0.4088 0.6145 0.632 0.000 NA 0.000 0.000
#> GSM152874 1 0.4088 0.6145 0.632 0.000 NA 0.000 0.000
#> GSM152875 1 0.4088 0.6145 0.632 0.000 NA 0.000 0.000
#> GSM152876 1 0.4238 0.6105 0.628 0.004 NA 0.000 0.000
#> GSM152877 1 0.4088 0.6145 0.632 0.000 NA 0.000 0.000
#> GSM152878 1 0.4088 0.6145 0.632 0.000 NA 0.000 0.000
#> GSM152879 1 0.4088 0.6145 0.632 0.000 NA 0.000 0.000
#> GSM152880 1 0.4088 0.6145 0.632 0.000 NA 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.1155 0.7129 0.000 0.956 NA 0.000 0.004 NA
#> GSM152805 5 0.0713 0.7017 0.000 0.028 NA 0.000 0.972 NA
#> GSM152806 5 0.0547 0.6990 0.000 0.020 NA 0.000 0.980 NA
#> GSM152807 2 0.1152 0.7123 0.000 0.952 NA 0.000 0.004 NA
#> GSM152808 5 0.0547 0.6990 0.000 0.020 NA 0.000 0.980 NA
#> GSM152809 2 0.1152 0.7123 0.000 0.952 NA 0.000 0.004 NA
#> GSM152810 5 0.3997 0.2656 0.000 0.000 NA 0.020 0.688 NA
#> GSM152811 5 0.3409 0.4752 0.000 0.008 NA 0.020 0.804 NA
#> GSM152812 2 0.1219 0.7123 0.000 0.948 NA 0.000 0.004 NA
#> GSM152813 2 0.1257 0.7133 0.000 0.952 NA 0.000 0.028 NA
#> GSM152814 2 0.1151 0.7130 0.000 0.956 NA 0.000 0.012 NA
#> GSM152815 2 0.1204 0.7114 0.000 0.944 NA 0.000 0.000 NA
#> GSM152816 2 0.5132 0.0848 0.000 0.512 NA 0.000 0.412 NA
#> GSM152817 5 0.0547 0.6990 0.000 0.020 NA 0.000 0.980 NA
#> GSM152818 5 0.0713 0.7017 0.000 0.028 NA 0.000 0.972 NA
#> GSM152819 2 0.5171 -0.0595 0.000 0.480 NA 0.000 0.448 NA
#> GSM152820 2 0.3233 0.7052 0.000 0.828 NA 0.000 0.024 NA
#> GSM152821 2 0.1434 0.7129 0.000 0.948 NA 0.000 0.020 NA
#> GSM153115 2 0.3930 0.5813 0.000 0.628 NA 0.004 0.000 NA
#> GSM153116 5 0.4905 0.5387 0.000 0.264 NA 0.000 0.640 NA
#> GSM153117 2 0.5151 0.4004 0.000 0.604 NA 0.000 0.296 NA
#> GSM153118 2 0.1518 0.7082 0.000 0.944 NA 0.000 0.024 NA
#> GSM153119 5 0.3943 0.6360 0.000 0.156 NA 0.000 0.760 NA
#> GSM153120 2 0.3996 0.4466 0.000 0.512 NA 0.000 0.000 NA
#> GSM153121 2 0.5035 0.4713 0.000 0.640 NA 0.000 0.168 NA
#> GSM153122 5 0.1003 0.6894 0.000 0.016 NA 0.000 0.964 NA
#> GSM153123 2 0.3054 0.6741 0.000 0.848 NA 0.000 0.076 NA
#> GSM153124 2 0.3716 0.6576 0.000 0.732 NA 0.000 0.008 NA
#> GSM153125 2 0.3804 0.5293 0.000 0.576 NA 0.000 0.000 NA
#> GSM153126 2 0.5568 0.3376 0.000 0.552 NA 0.000 0.212 NA
#> GSM153127 2 0.1858 0.7073 0.000 0.904 NA 0.000 0.000 NA
#> GSM153128 2 0.5069 0.4482 0.000 0.628 NA 0.000 0.144 NA
#> GSM153129 2 0.3513 0.6750 0.000 0.816 NA 0.000 0.072 NA
#> GSM153130 2 0.5684 0.2890 0.000 0.528 NA 0.000 0.244 NA
#> GSM153131 2 0.3816 0.6471 0.000 0.792 NA 0.000 0.096 NA
#> GSM153132 2 0.3806 0.6233 0.000 0.772 NA 0.000 0.152 NA
#> GSM153133 2 0.2593 0.6974 0.000 0.884 NA 0.000 0.036 NA
#> GSM153134 2 0.2515 0.7026 0.000 0.892 NA 0.000 0.052 NA
#> GSM153135 2 0.1908 0.7075 0.000 0.900 NA 0.000 0.000 NA
#> GSM153136 2 0.3833 0.5066 0.000 0.556 NA 0.000 0.000 NA
#> GSM153137 2 0.2302 0.7024 0.000 0.872 NA 0.000 0.000 NA
#> GSM153138 2 0.1152 0.7140 0.000 0.952 NA 0.000 0.004 NA
#> GSM153139 2 0.5684 0.2890 0.000 0.528 NA 0.000 0.244 NA
#> GSM153140 2 0.2563 0.7171 0.000 0.892 NA 0.000 0.036 NA
#> GSM153141 2 0.1700 0.7097 0.000 0.916 NA 0.000 0.000 NA
#> GSM153142 5 0.3772 0.6401 0.000 0.160 NA 0.000 0.772 NA
#> GSM153143 2 0.2162 0.7143 0.000 0.896 NA 0.000 0.004 NA
#> GSM153144 2 0.3510 0.6680 0.000 0.820 NA 0.000 0.068 NA
#> GSM153145 5 0.0547 0.6990 0.000 0.020 NA 0.000 0.980 NA
#> GSM153146 2 0.1635 0.7111 0.000 0.940 NA 0.000 0.020 NA
#> GSM153147 2 0.3820 0.6530 0.000 0.796 NA 0.000 0.092 NA
#> GSM153148 2 0.1858 0.7073 0.000 0.904 NA 0.000 0.000 NA
#> GSM153149 2 0.2183 0.7096 0.000 0.912 NA 0.000 0.028 NA
#> GSM153150 2 0.3838 0.5033 0.000 0.552 NA 0.000 0.000 NA
#> GSM153151 2 0.3852 0.6418 0.000 0.788 NA 0.000 0.088 NA
#> GSM153152 2 0.2965 0.6684 0.000 0.848 NA 0.000 0.072 NA
#> GSM153153 2 0.1875 0.7136 0.000 0.928 NA 0.000 0.032 NA
#> GSM153154 2 0.3956 0.6229 0.000 0.760 NA 0.000 0.152 NA
#> GSM153155 2 0.1620 0.7086 0.000 0.940 NA 0.000 0.024 NA
#> GSM153156 2 0.5113 0.4560 0.000 0.628 NA 0.000 0.168 NA
#> GSM153157 5 0.4931 0.5446 0.000 0.248 NA 0.000 0.636 NA
#> GSM153158 5 0.5422 0.1024 0.000 0.436 NA 0.000 0.460 NA
#> GSM153159 5 0.4125 0.6102 0.000 0.184 NA 0.000 0.736 NA
#> GSM153160 2 0.5568 0.3376 0.000 0.552 NA 0.000 0.212 NA
#> GSM153161 2 0.2165 0.7053 0.000 0.884 NA 0.000 0.000 NA
#> GSM153162 2 0.3618 0.6633 0.000 0.812 NA 0.000 0.076 NA
#> GSM153163 2 0.5684 0.2890 0.000 0.528 NA 0.000 0.244 NA
#> GSM153164 2 0.5135 0.4060 0.000 0.608 NA 0.000 0.292 NA
#> GSM153165 2 0.5685 0.2915 0.000 0.528 NA 0.000 0.240 NA
#> GSM153166 2 0.2278 0.7054 0.000 0.904 NA 0.000 0.052 NA
#> GSM153167 2 0.2444 0.7038 0.000 0.896 NA 0.000 0.052 NA
#> GSM153168 5 0.0692 0.6980 0.000 0.020 NA 0.000 0.976 NA
#> GSM153169 2 0.5692 0.2757 0.000 0.524 NA 0.000 0.260 NA
#> GSM153170 2 0.5667 0.3030 0.000 0.532 NA 0.000 0.236 NA
#> GSM153171 2 0.3858 0.6217 0.000 0.680 NA 0.004 0.004 NA
#> GSM153172 2 0.1882 0.7156 0.000 0.928 NA 0.000 0.024 NA
#> GSM153173 2 0.5684 0.2890 0.000 0.528 NA 0.000 0.244 NA
#> GSM153174 2 0.3565 0.6653 0.000 0.816 NA 0.000 0.072 NA
#> GSM153175 2 0.4187 0.5877 0.000 0.624 NA 0.000 0.004 NA
#> GSM153176 2 0.4429 0.6665 0.000 0.732 NA 0.000 0.040 NA
#> GSM153177 2 0.3622 0.6472 0.000 0.800 NA 0.000 0.124 NA
#> GSM152931 2 0.4032 0.5314 0.000 0.572 NA 0.000 0.000 NA
#> GSM152932 2 0.1959 0.7128 0.000 0.924 NA 0.000 0.032 NA
#> GSM152933 2 0.1434 0.7078 0.000 0.948 NA 0.000 0.024 NA
#> GSM152934 2 0.3776 0.7024 0.000 0.792 NA 0.000 0.024 NA
#> GSM152935 2 0.4110 0.6417 0.000 0.780 NA 0.008 0.096 NA
#> GSM152936 2 0.3619 0.6213 0.000 0.680 NA 0.000 0.004 NA
#> GSM152937 2 0.5002 0.4582 0.000 0.636 NA 0.000 0.136 NA
#> GSM152938 2 0.5047 0.4526 0.000 0.628 NA 0.000 0.136 NA
#> GSM152939 2 0.4127 0.6962 0.000 0.780 NA 0.000 0.040 NA
#> GSM152940 2 0.3867 0.4437 0.000 0.512 NA 0.000 0.000 NA
#> GSM152941 1 0.6575 -0.0276 0.540 0.020 NA 0.052 0.000 NA
#> GSM152942 2 0.5062 0.5515 0.000 0.676 NA 0.000 0.152 NA
#> GSM152943 2 0.2604 0.7122 0.000 0.872 NA 0.008 0.000 NA
#> GSM152944 2 0.5571 0.3415 0.000 0.552 NA 0.000 0.228 NA
#> GSM152945 2 0.6179 -0.0226 0.000 0.452 NA 0.028 0.004 NA
#> GSM152946 2 0.3300 0.7144 0.000 0.832 NA 0.000 0.020 NA
#> GSM152947 2 0.3955 0.5090 0.000 0.560 NA 0.004 0.000 NA
#> GSM152948 2 0.2349 0.7190 0.000 0.892 NA 0.000 0.008 NA
#> GSM152949 2 0.3325 0.6575 0.000 0.820 NA 0.000 0.084 NA
#> GSM152950 2 0.3372 0.6557 0.000 0.816 NA 0.000 0.100 NA
#> GSM152951 2 0.1890 0.7190 0.000 0.924 NA 0.000 0.008 NA
#> GSM152952 2 0.1908 0.7070 0.000 0.900 NA 0.000 0.000 NA
#> GSM152953 2 0.1204 0.7126 0.000 0.944 NA 0.000 0.000 NA
#> GSM152954 2 0.3961 0.5063 0.000 0.556 NA 0.004 0.000 NA
#> GSM152955 2 0.3952 0.6655 0.000 0.800 NA 0.008 0.072 NA
#> GSM152956 2 0.1663 0.7079 0.000 0.912 NA 0.000 0.000 NA
#> GSM152957 2 0.3672 0.5790 0.000 0.632 NA 0.000 0.000 NA
#> GSM152958 2 0.3833 0.5066 0.000 0.556 NA 0.000 0.000 NA
#> GSM152959 2 0.4082 0.5161 0.000 0.560 NA 0.004 0.000 NA
#> GSM152960 2 0.3841 0.5677 0.000 0.616 NA 0.000 0.000 NA
#> GSM152961 2 0.4127 0.4353 0.004 0.508 NA 0.004 0.000 NA
#> GSM152962 2 0.3785 0.6345 0.000 0.788 NA 0.000 0.088 NA
#> GSM152963 2 0.1714 0.7075 0.000 0.908 NA 0.000 0.000 NA
#> GSM152964 5 0.6399 0.3853 0.000 0.332 NA 0.008 0.420 NA
#> GSM152965 2 0.2401 0.7083 0.000 0.900 NA 0.000 0.044 NA
#> GSM152966 2 0.3804 0.5293 0.000 0.576 NA 0.000 0.000 NA
#> GSM152967 2 0.2822 0.6835 0.000 0.864 NA 0.000 0.056 NA
#> GSM152968 2 0.3520 0.6482 0.000 0.804 NA 0.000 0.100 NA
#> GSM152969 2 0.3804 0.5293 0.000 0.576 NA 0.000 0.000 NA
#> GSM152970 2 0.3930 0.5787 0.004 0.628 NA 0.004 0.000 NA
#> GSM152971 2 0.3804 0.5293 0.000 0.576 NA 0.000 0.000 NA
#> GSM152972 2 0.3817 0.5208 0.000 0.568 NA 0.000 0.000 NA
#> GSM152973 2 0.4682 0.6747 0.000 0.748 NA 0.000 0.072 NA
#> GSM152974 2 0.1991 0.7112 0.000 0.920 NA 0.000 0.024 NA
#> GSM152975 2 0.3667 0.6877 0.000 0.788 NA 0.000 0.044 NA
#> GSM152976 2 0.3809 0.6194 0.000 0.684 NA 0.000 0.008 NA
#> GSM152977 2 0.4194 0.6172 0.000 0.664 NA 0.000 0.020 NA
#> GSM152978 2 0.3971 0.4959 0.000 0.548 NA 0.004 0.000 NA
#> GSM152979 2 0.5630 0.3204 0.000 0.540 NA 0.000 0.228 NA
#> GSM152980 2 0.3159 0.6978 0.000 0.820 NA 0.000 0.020 NA
#> GSM152981 5 0.0692 0.6980 0.000 0.020 NA 0.000 0.976 NA
#> GSM152982 2 0.4213 0.6025 0.000 0.636 NA 0.000 0.020 NA
#> GSM152983 2 0.3747 0.5555 0.000 0.604 NA 0.000 0.000 NA
#> GSM152984 2 0.4144 0.6953 0.000 0.788 NA 0.000 0.048 NA
#> GSM152985 2 0.3996 0.4411 0.000 0.512 NA 0.004 0.000 NA
#> GSM152986 2 0.3804 0.5289 0.000 0.576 NA 0.000 0.000 NA
#> GSM152987 4 0.7038 0.0000 0.096 0.000 NA 0.408 0.000 NA
#> GSM152988 2 0.4151 0.7029 0.000 0.788 NA 0.000 0.068 NA
#> GSM152989 2 0.3727 0.5626 0.000 0.612 NA 0.000 0.000 NA
#> GSM152990 2 0.5530 0.3556 0.000 0.560 NA 0.000 0.224 NA
#> GSM152991 2 0.5246 0.3162 0.000 0.588 NA 0.000 0.296 NA
#> GSM187524 1 0.6134 0.1321 0.580 0.000 NA 0.068 0.000 NA
#> GSM187525 1 0.6192 0.1103 0.568 0.000 NA 0.064 0.000 NA
#> GSM187526 1 0.5785 0.1412 0.620 0.000 NA 0.056 0.000 NA
#> GSM187527 1 0.4227 0.5689 0.496 0.008 NA 0.492 0.000 NA
#> GSM152856 1 0.3868 0.5804 0.504 0.000 NA 0.496 0.000 NA
#> GSM152857 1 0.4098 0.5707 0.496 0.008 NA 0.496 0.000 NA
#> GSM152858 1 0.2189 0.5853 0.904 0.000 NA 0.004 0.000 NA
#> GSM152859 1 0.6668 -0.1236 0.492 0.000 NA 0.040 0.012 NA
#> GSM152860 1 0.2189 0.5853 0.904 0.000 NA 0.004 0.000 NA
#> GSM152861 1 0.0725 0.6045 0.976 0.000 NA 0.012 0.000 NA
#> GSM152862 1 0.2189 0.5853 0.904 0.000 NA 0.004 0.000 NA
#> GSM152863 1 0.3215 0.6059 0.756 0.004 NA 0.240 0.000 NA
#> GSM152864 1 0.0725 0.6045 0.976 0.000 NA 0.012 0.000 NA
#> GSM152865 1 0.0725 0.6045 0.976 0.000 NA 0.012 0.000 NA
#> GSM152866 1 0.3868 0.5797 0.504 0.000 NA 0.496 0.000 NA
#> GSM152867 1 0.0725 0.6045 0.976 0.000 NA 0.012 0.000 NA
#> GSM152868 1 0.0725 0.6045 0.976 0.000 NA 0.012 0.000 NA
#> GSM152869 1 0.0725 0.6045 0.976 0.000 NA 0.012 0.000 NA
#> GSM152870 1 0.2189 0.5853 0.904 0.000 NA 0.004 0.000 NA
#> GSM152871 1 0.2189 0.5853 0.904 0.000 NA 0.004 0.000 NA
#> GSM152872 1 0.2189 0.5853 0.904 0.000 NA 0.004 0.000 NA
#> GSM152873 1 0.3868 0.5804 0.504 0.000 NA 0.496 0.000 NA
#> GSM152874 1 0.3868 0.5804 0.504 0.000 NA 0.496 0.000 NA
#> GSM152875 1 0.3868 0.5804 0.504 0.000 NA 0.496 0.000 NA
#> GSM152876 1 0.3998 0.5780 0.504 0.004 NA 0.492 0.000 NA
#> GSM152877 1 0.3868 0.5804 0.504 0.000 NA 0.496 0.000 NA
#> GSM152878 1 0.3868 0.5804 0.504 0.000 NA 0.496 0.000 NA
#> GSM152879 1 0.3868 0.5804 0.504 0.000 NA 0.496 0.000 NA
#> GSM152880 1 0.3868 0.5804 0.504 0.000 NA 0.496 0.000 NA
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> SD:hclust 171 6.38e-29 2
#> SD:hclust 163 3.48e-32 3
#> SD:hclust 161 6.04e-36 4
#> SD:hclust 157 2.15e-34 5
#> SD:hclust 133 5.49e-28 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "kmeans"]
# you can also extract it by
# res = res_list["SD:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.992 0.996 0.3179 0.687 0.687
#> 3 3 0.809 0.925 0.943 0.8999 0.669 0.525
#> 4 4 0.626 0.369 0.610 0.1520 0.878 0.714
#> 5 5 0.689 0.765 0.781 0.0797 0.778 0.434
#> 6 6 0.717 0.757 0.842 0.0570 0.987 0.939
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.996 0.000 1.000
#> GSM152805 2 0.0000 0.996 0.000 1.000
#> GSM152806 2 0.0000 0.996 0.000 1.000
#> GSM152807 2 0.0000 0.996 0.000 1.000
#> GSM152808 2 0.0000 0.996 0.000 1.000
#> GSM152809 2 0.0000 0.996 0.000 1.000
#> GSM152810 2 0.0000 0.996 0.000 1.000
#> GSM152811 2 0.0000 0.996 0.000 1.000
#> GSM152812 2 0.0000 0.996 0.000 1.000
#> GSM152813 2 0.0000 0.996 0.000 1.000
#> GSM152814 2 0.0000 0.996 0.000 1.000
#> GSM152815 2 0.0000 0.996 0.000 1.000
#> GSM152816 2 0.0000 0.996 0.000 1.000
#> GSM152817 2 0.0000 0.996 0.000 1.000
#> GSM152818 2 0.0000 0.996 0.000 1.000
#> GSM152819 2 0.0000 0.996 0.000 1.000
#> GSM152820 2 0.0000 0.996 0.000 1.000
#> GSM152821 2 0.0000 0.996 0.000 1.000
#> GSM153115 2 0.0000 0.996 0.000 1.000
#> GSM153116 2 0.0000 0.996 0.000 1.000
#> GSM153117 2 0.0000 0.996 0.000 1.000
#> GSM153118 2 0.0000 0.996 0.000 1.000
#> GSM153119 2 0.0000 0.996 0.000 1.000
#> GSM153120 2 0.0376 0.992 0.004 0.996
#> GSM153121 2 0.0000 0.996 0.000 1.000
#> GSM153122 2 0.0000 0.996 0.000 1.000
#> GSM153123 2 0.0000 0.996 0.000 1.000
#> GSM153124 2 0.0000 0.996 0.000 1.000
#> GSM153125 2 0.0000 0.996 0.000 1.000
#> GSM153126 2 0.0000 0.996 0.000 1.000
#> GSM153127 2 0.0000 0.996 0.000 1.000
#> GSM153128 2 0.0000 0.996 0.000 1.000
#> GSM153129 2 0.0000 0.996 0.000 1.000
#> GSM153130 2 0.0000 0.996 0.000 1.000
#> GSM153131 2 0.0000 0.996 0.000 1.000
#> GSM153132 2 0.0000 0.996 0.000 1.000
#> GSM153133 2 0.0000 0.996 0.000 1.000
#> GSM153134 2 0.0000 0.996 0.000 1.000
#> GSM153135 2 0.0000 0.996 0.000 1.000
#> GSM153136 2 0.0000 0.996 0.000 1.000
#> GSM153137 2 0.0000 0.996 0.000 1.000
#> GSM153138 2 0.0000 0.996 0.000 1.000
#> GSM153139 2 0.0000 0.996 0.000 1.000
#> GSM153140 2 0.0000 0.996 0.000 1.000
#> GSM153141 2 0.0000 0.996 0.000 1.000
#> GSM153142 2 0.0000 0.996 0.000 1.000
#> GSM153143 2 0.0000 0.996 0.000 1.000
#> GSM153144 2 0.0000 0.996 0.000 1.000
#> GSM153145 2 0.0000 0.996 0.000 1.000
#> GSM153146 2 0.0000 0.996 0.000 1.000
#> GSM153147 2 0.0000 0.996 0.000 1.000
#> GSM153148 2 0.0000 0.996 0.000 1.000
#> GSM153149 2 0.0000 0.996 0.000 1.000
#> GSM153150 2 0.0000 0.996 0.000 1.000
#> GSM153151 2 0.0000 0.996 0.000 1.000
#> GSM153152 2 0.0000 0.996 0.000 1.000
#> GSM153153 2 0.0000 0.996 0.000 1.000
#> GSM153154 2 0.0000 0.996 0.000 1.000
#> GSM153155 2 0.0000 0.996 0.000 1.000
#> GSM153156 2 0.0000 0.996 0.000 1.000
#> GSM153157 2 0.0000 0.996 0.000 1.000
#> GSM153158 2 0.0000 0.996 0.000 1.000
#> GSM153159 2 0.0000 0.996 0.000 1.000
#> GSM153160 2 0.0000 0.996 0.000 1.000
#> GSM153161 2 0.0000 0.996 0.000 1.000
#> GSM153162 2 0.0000 0.996 0.000 1.000
#> GSM153163 2 0.0000 0.996 0.000 1.000
#> GSM153164 2 0.0000 0.996 0.000 1.000
#> GSM153165 2 0.0000 0.996 0.000 1.000
#> GSM153166 2 0.0000 0.996 0.000 1.000
#> GSM153167 2 0.0000 0.996 0.000 1.000
#> GSM153168 2 0.0000 0.996 0.000 1.000
#> GSM153169 2 0.0000 0.996 0.000 1.000
#> GSM153170 2 0.0000 0.996 0.000 1.000
#> GSM153171 2 0.0000 0.996 0.000 1.000
#> GSM153172 2 0.0000 0.996 0.000 1.000
#> GSM153173 2 0.0000 0.996 0.000 1.000
#> GSM153174 2 0.0000 0.996 0.000 1.000
#> GSM153175 2 0.0000 0.996 0.000 1.000
#> GSM153176 2 0.0000 0.996 0.000 1.000
#> GSM153177 2 0.0000 0.996 0.000 1.000
#> GSM152931 2 0.0000 0.996 0.000 1.000
#> GSM152932 2 0.0000 0.996 0.000 1.000
#> GSM152933 2 0.0000 0.996 0.000 1.000
#> GSM152934 2 0.0000 0.996 0.000 1.000
#> GSM152935 2 0.0000 0.996 0.000 1.000
#> GSM152936 2 0.0000 0.996 0.000 1.000
#> GSM152937 2 0.0000 0.996 0.000 1.000
#> GSM152938 2 0.0000 0.996 0.000 1.000
#> GSM152939 2 0.0000 0.996 0.000 1.000
#> GSM152940 2 0.3879 0.917 0.076 0.924
#> GSM152941 1 0.0000 0.999 1.000 0.000
#> GSM152942 2 0.0000 0.996 0.000 1.000
#> GSM152943 2 0.0000 0.996 0.000 1.000
#> GSM152944 2 0.0000 0.996 0.000 1.000
#> GSM152945 2 0.0000 0.996 0.000 1.000
#> GSM152946 2 0.0000 0.996 0.000 1.000
#> GSM152947 2 0.0000 0.996 0.000 1.000
#> GSM152948 2 0.0000 0.996 0.000 1.000
#> GSM152949 2 0.0000 0.996 0.000 1.000
#> GSM152950 2 0.0000 0.996 0.000 1.000
#> GSM152951 2 0.0000 0.996 0.000 1.000
#> GSM152952 2 0.0000 0.996 0.000 1.000
#> GSM152953 2 0.0000 0.996 0.000 1.000
#> GSM152954 2 0.0000 0.996 0.000 1.000
#> GSM152955 2 0.0000 0.996 0.000 1.000
#> GSM152956 2 0.0000 0.996 0.000 1.000
#> GSM152957 2 0.0000 0.996 0.000 1.000
#> GSM152958 2 0.6343 0.811 0.160 0.840
#> GSM152959 2 0.0672 0.988 0.008 0.992
#> GSM152960 2 0.0000 0.996 0.000 1.000
#> GSM152961 2 0.8955 0.552 0.312 0.688
#> GSM152962 2 0.0000 0.996 0.000 1.000
#> GSM152963 2 0.0000 0.996 0.000 1.000
#> GSM152964 2 0.0000 0.996 0.000 1.000
#> GSM152965 2 0.0000 0.996 0.000 1.000
#> GSM152966 2 0.0000 0.996 0.000 1.000
#> GSM152967 2 0.0000 0.996 0.000 1.000
#> GSM152968 2 0.0000 0.996 0.000 1.000
#> GSM152969 2 0.0000 0.996 0.000 1.000
#> GSM152970 2 0.2423 0.956 0.040 0.960
#> GSM152971 2 0.0000 0.996 0.000 1.000
#> GSM152972 2 0.0000 0.996 0.000 1.000
#> GSM152973 2 0.0000 0.996 0.000 1.000
#> GSM152974 2 0.0000 0.996 0.000 1.000
#> GSM152975 2 0.0000 0.996 0.000 1.000
#> GSM152976 2 0.0000 0.996 0.000 1.000
#> GSM152977 2 0.0000 0.996 0.000 1.000
#> GSM152978 2 0.0000 0.996 0.000 1.000
#> GSM152979 2 0.0000 0.996 0.000 1.000
#> GSM152980 2 0.0000 0.996 0.000 1.000
#> GSM152981 2 0.0000 0.996 0.000 1.000
#> GSM152982 2 0.0000 0.996 0.000 1.000
#> GSM152983 2 0.0000 0.996 0.000 1.000
#> GSM152984 2 0.0000 0.996 0.000 1.000
#> GSM152985 1 0.0000 0.999 1.000 0.000
#> GSM152986 2 0.0000 0.996 0.000 1.000
#> GSM152987 1 0.0000 0.999 1.000 0.000
#> GSM152988 2 0.0000 0.996 0.000 1.000
#> GSM152989 1 0.2423 0.958 0.960 0.040
#> GSM152990 2 0.0000 0.996 0.000 1.000
#> GSM152991 2 0.0000 0.996 0.000 1.000
#> GSM187524 1 0.0000 0.999 1.000 0.000
#> GSM187525 1 0.0000 0.999 1.000 0.000
#> GSM187526 1 0.0000 0.999 1.000 0.000
#> GSM187527 1 0.0000 0.999 1.000 0.000
#> GSM152856 1 0.0000 0.999 1.000 0.000
#> GSM152857 1 0.0000 0.999 1.000 0.000
#> GSM152858 1 0.0000 0.999 1.000 0.000
#> GSM152859 1 0.0000 0.999 1.000 0.000
#> GSM152860 1 0.0000 0.999 1.000 0.000
#> GSM152861 1 0.0000 0.999 1.000 0.000
#> GSM152862 1 0.0000 0.999 1.000 0.000
#> GSM152863 1 0.0000 0.999 1.000 0.000
#> GSM152864 1 0.0000 0.999 1.000 0.000
#> GSM152865 1 0.0000 0.999 1.000 0.000
#> GSM152866 1 0.0000 0.999 1.000 0.000
#> GSM152867 1 0.0000 0.999 1.000 0.000
#> GSM152868 1 0.0000 0.999 1.000 0.000
#> GSM152869 1 0.0000 0.999 1.000 0.000
#> GSM152870 1 0.0000 0.999 1.000 0.000
#> GSM152871 1 0.0000 0.999 1.000 0.000
#> GSM152872 1 0.0000 0.999 1.000 0.000
#> GSM152873 1 0.0000 0.999 1.000 0.000
#> GSM152874 1 0.0000 0.999 1.000 0.000
#> GSM152875 1 0.0000 0.999 1.000 0.000
#> GSM152876 1 0.0000 0.999 1.000 0.000
#> GSM152877 1 0.0000 0.999 1.000 0.000
#> GSM152878 1 0.0000 0.999 1.000 0.000
#> GSM152879 1 0.0000 0.999 1.000 0.000
#> GSM152880 1 0.0000 0.999 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152805 3 0.1753 0.952 0.000 0.048 0.952
#> GSM152806 3 0.1753 0.952 0.000 0.048 0.952
#> GSM152807 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152808 3 0.1753 0.952 0.000 0.048 0.952
#> GSM152809 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152810 3 0.1529 0.935 0.000 0.040 0.960
#> GSM152811 3 0.1753 0.952 0.000 0.048 0.952
#> GSM152812 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152813 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152814 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152815 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152816 3 0.1753 0.952 0.000 0.048 0.952
#> GSM152817 3 0.1753 0.952 0.000 0.048 0.952
#> GSM152818 3 0.1753 0.952 0.000 0.048 0.952
#> GSM152819 3 0.1753 0.952 0.000 0.048 0.952
#> GSM152820 3 0.2261 0.941 0.000 0.068 0.932
#> GSM152821 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153115 2 0.0237 0.943 0.000 0.996 0.004
#> GSM153116 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153117 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153118 2 0.2959 0.908 0.000 0.900 0.100
#> GSM153119 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153120 2 0.0661 0.933 0.008 0.988 0.004
#> GSM153121 3 0.1860 0.950 0.000 0.052 0.948
#> GSM153122 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153123 2 0.2537 0.929 0.000 0.920 0.080
#> GSM153124 2 0.0237 0.943 0.000 0.996 0.004
#> GSM153125 2 0.0237 0.943 0.000 0.996 0.004
#> GSM153126 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153127 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153128 3 0.1860 0.950 0.000 0.052 0.948
#> GSM153129 3 0.6045 0.461 0.000 0.380 0.620
#> GSM153130 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153131 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153132 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153133 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153134 3 0.5968 0.501 0.000 0.364 0.636
#> GSM153135 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153136 2 0.0237 0.943 0.000 0.996 0.004
#> GSM153137 2 0.0892 0.946 0.000 0.980 0.020
#> GSM153138 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153139 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153140 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153141 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153142 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153143 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153144 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153145 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153146 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153147 2 0.5926 0.454 0.000 0.644 0.356
#> GSM153148 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153149 2 0.2796 0.917 0.000 0.908 0.092
#> GSM153150 2 0.0000 0.941 0.000 1.000 0.000
#> GSM153151 2 0.2796 0.917 0.000 0.908 0.092
#> GSM153152 3 0.5926 0.521 0.000 0.356 0.644
#> GSM153153 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153154 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153155 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153156 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153157 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153158 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153159 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153160 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153161 2 0.1643 0.947 0.000 0.956 0.044
#> GSM153162 3 0.3619 0.881 0.000 0.136 0.864
#> GSM153163 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153164 3 0.3879 0.859 0.000 0.152 0.848
#> GSM153165 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153166 2 0.6045 0.386 0.000 0.620 0.380
#> GSM153167 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153168 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153169 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153170 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153171 2 0.0000 0.941 0.000 1.000 0.000
#> GSM153172 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153173 3 0.1753 0.952 0.000 0.048 0.952
#> GSM153174 2 0.1964 0.948 0.000 0.944 0.056
#> GSM153175 2 0.0237 0.943 0.000 0.996 0.004
#> GSM153176 3 0.6062 0.522 0.000 0.384 0.616
#> GSM153177 2 0.6252 0.169 0.000 0.556 0.444
#> GSM152931 2 0.0237 0.943 0.000 0.996 0.004
#> GSM152932 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152933 2 0.5497 0.605 0.000 0.708 0.292
#> GSM152934 2 0.0424 0.944 0.000 0.992 0.008
#> GSM152935 3 0.3551 0.882 0.000 0.132 0.868
#> GSM152936 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152937 3 0.2537 0.931 0.000 0.080 0.920
#> GSM152938 3 0.3038 0.911 0.000 0.104 0.896
#> GSM152939 2 0.0237 0.943 0.000 0.996 0.004
#> GSM152940 2 0.0829 0.929 0.012 0.984 0.004
#> GSM152941 1 0.0829 0.987 0.984 0.004 0.012
#> GSM152942 3 0.2537 0.932 0.000 0.080 0.920
#> GSM152943 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152944 3 0.1753 0.952 0.000 0.048 0.952
#> GSM152945 2 0.2165 0.942 0.000 0.936 0.064
#> GSM152946 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152947 2 0.0237 0.939 0.000 0.996 0.004
#> GSM152948 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152949 3 0.2165 0.943 0.000 0.064 0.936
#> GSM152950 3 0.2796 0.922 0.000 0.092 0.908
#> GSM152951 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152952 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152953 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152954 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152955 3 0.5465 0.659 0.000 0.288 0.712
#> GSM152956 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152957 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152958 2 0.0829 0.929 0.012 0.984 0.004
#> GSM152959 2 0.0237 0.939 0.000 0.996 0.004
#> GSM152960 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152961 2 0.0829 0.929 0.012 0.984 0.004
#> GSM152962 3 0.3482 0.890 0.000 0.128 0.872
#> GSM152963 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152964 3 0.1860 0.948 0.000 0.052 0.948
#> GSM152965 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152966 2 0.0237 0.943 0.000 0.996 0.004
#> GSM152967 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152968 3 0.2261 0.940 0.000 0.068 0.932
#> GSM152969 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152970 2 0.0237 0.939 0.000 0.996 0.004
#> GSM152971 2 0.0237 0.943 0.000 0.996 0.004
#> GSM152972 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152973 2 0.0237 0.943 0.000 0.996 0.004
#> GSM152974 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152975 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152976 2 0.0237 0.943 0.000 0.996 0.004
#> GSM152977 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152978 2 0.0237 0.939 0.000 0.996 0.004
#> GSM152979 3 0.1753 0.952 0.000 0.048 0.952
#> GSM152980 2 0.1529 0.947 0.000 0.960 0.040
#> GSM152981 3 0.1753 0.952 0.000 0.048 0.952
#> GSM152982 2 0.0237 0.943 0.000 0.996 0.004
#> GSM152983 2 0.0237 0.943 0.000 0.996 0.004
#> GSM152984 2 0.1964 0.948 0.000 0.944 0.056
#> GSM152985 2 0.4861 0.731 0.180 0.808 0.012
#> GSM152986 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152987 1 0.0829 0.987 0.984 0.004 0.012
#> GSM152988 2 0.0237 0.943 0.000 0.996 0.004
#> GSM152989 2 0.2096 0.894 0.052 0.944 0.004
#> GSM152990 3 0.1753 0.952 0.000 0.048 0.952
#> GSM152991 3 0.1753 0.952 0.000 0.048 0.952
#> GSM187524 1 0.1129 0.985 0.976 0.004 0.020
#> GSM187525 1 0.1129 0.985 0.976 0.004 0.020
#> GSM187526 1 0.0829 0.987 0.984 0.004 0.012
#> GSM187527 1 0.0892 0.987 0.980 0.000 0.020
#> GSM152856 1 0.0892 0.987 0.980 0.000 0.020
#> GSM152857 1 0.0892 0.987 0.980 0.000 0.020
#> GSM152858 1 0.1399 0.984 0.968 0.004 0.028
#> GSM152859 1 0.1399 0.984 0.968 0.004 0.028
#> GSM152860 1 0.1399 0.984 0.968 0.004 0.028
#> GSM152861 1 0.0000 0.989 1.000 0.000 0.000
#> GSM152862 1 0.1399 0.984 0.968 0.004 0.028
#> GSM152863 1 0.0000 0.989 1.000 0.000 0.000
#> GSM152864 1 0.0000 0.989 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.989 1.000 0.000 0.000
#> GSM152866 1 0.0892 0.987 0.980 0.000 0.020
#> GSM152867 1 0.0000 0.989 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.989 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.989 1.000 0.000 0.000
#> GSM152870 1 0.1399 0.984 0.968 0.004 0.028
#> GSM152871 1 0.1399 0.984 0.968 0.004 0.028
#> GSM152872 1 0.1399 0.984 0.968 0.004 0.028
#> GSM152873 1 0.0892 0.987 0.980 0.000 0.020
#> GSM152874 1 0.0892 0.987 0.980 0.000 0.020
#> GSM152875 1 0.0892 0.987 0.980 0.000 0.020
#> GSM152876 1 0.0892 0.987 0.980 0.000 0.020
#> GSM152877 1 0.0892 0.987 0.980 0.000 0.020
#> GSM152878 1 0.0892 0.987 0.980 0.000 0.020
#> GSM152879 1 0.0892 0.987 0.980 0.000 0.020
#> GSM152880 1 0.0892 0.987 0.980 0.000 0.020
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.4679 -0.1100 0.000 0.648 0.000 0.352
#> GSM152805 3 0.0336 0.5874 0.000 0.008 0.992 0.000
#> GSM152806 3 0.0336 0.5874 0.000 0.008 0.992 0.000
#> GSM152807 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM152808 3 0.0336 0.5874 0.000 0.008 0.992 0.000
#> GSM152809 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM152810 3 0.1637 0.5420 0.000 0.000 0.940 0.060
#> GSM152811 3 0.0336 0.5874 0.000 0.008 0.992 0.000
#> GSM152812 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM152813 2 0.4746 -0.1349 0.000 0.632 0.000 0.368
#> GSM152814 2 0.4730 -0.1286 0.000 0.636 0.000 0.364
#> GSM152815 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM152816 3 0.7275 0.0384 0.000 0.152 0.472 0.376
#> GSM152817 3 0.0336 0.5874 0.000 0.008 0.992 0.000
#> GSM152818 3 0.0336 0.5874 0.000 0.008 0.992 0.000
#> GSM152819 2 0.7847 -0.6372 0.000 0.384 0.268 0.348
#> GSM152820 2 0.7697 -0.6124 0.000 0.404 0.220 0.376
#> GSM152821 2 0.4730 -0.1286 0.000 0.636 0.000 0.364
#> GSM153115 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM153116 3 0.3335 0.5342 0.000 0.020 0.860 0.120
#> GSM153117 4 0.7921 0.4056 0.000 0.320 0.332 0.348
#> GSM153118 2 0.4936 -0.1517 0.000 0.624 0.004 0.372
#> GSM153119 3 0.1151 0.5782 0.000 0.008 0.968 0.024
#> GSM153120 2 0.4941 0.4645 0.000 0.564 0.000 0.436
#> GSM153121 3 0.7621 -0.2059 0.000 0.204 0.420 0.376
#> GSM153122 3 0.1151 0.5782 0.000 0.008 0.968 0.024
#> GSM153123 2 0.4950 -0.1600 0.000 0.620 0.004 0.376
#> GSM153124 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM153125 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM153126 3 0.6500 0.2643 0.000 0.080 0.544 0.376
#> GSM153127 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM153128 4 0.7666 0.1916 0.000 0.212 0.392 0.396
#> GSM153129 2 0.7172 -0.4771 0.000 0.484 0.140 0.376
#> GSM153130 3 0.5997 0.3106 0.000 0.048 0.576 0.376
#> GSM153131 4 0.7842 0.3527 0.000 0.264 0.360 0.376
#> GSM153132 4 0.7872 0.4869 0.000 0.344 0.280 0.376
#> GSM153133 2 0.4776 -0.1496 0.000 0.624 0.000 0.376
#> GSM153134 2 0.7060 -0.4519 0.000 0.496 0.128 0.376
#> GSM153135 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM153136 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM153137 2 0.0921 0.4368 0.000 0.972 0.000 0.028
#> GSM153138 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM153139 3 0.7060 0.1364 0.000 0.128 0.496 0.376
#> GSM153140 2 0.0336 0.4245 0.000 0.992 0.000 0.008
#> GSM153141 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM153142 3 0.0336 0.5874 0.000 0.008 0.992 0.000
#> GSM153143 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM153144 2 0.4776 -0.1496 0.000 0.624 0.000 0.376
#> GSM153145 3 0.0336 0.5874 0.000 0.008 0.992 0.000
#> GSM153146 2 0.4746 -0.1349 0.000 0.632 0.000 0.368
#> GSM153147 2 0.6386 -0.3289 0.000 0.552 0.072 0.376
#> GSM153148 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM153149 2 0.5204 -0.1812 0.000 0.612 0.012 0.376
#> GSM153150 2 0.4941 0.4645 0.000 0.564 0.000 0.436
#> GSM153151 2 0.5016 -0.1927 0.000 0.600 0.004 0.396
#> GSM153152 2 0.7136 -0.4686 0.000 0.488 0.136 0.376
#> GSM153153 2 0.4761 -0.1420 0.000 0.628 0.000 0.372
#> GSM153154 3 0.7506 -0.1121 0.000 0.184 0.440 0.376
#> GSM153155 2 0.4624 -0.0913 0.000 0.660 0.000 0.340
#> GSM153156 3 0.7426 -0.0563 0.000 0.172 0.452 0.376
#> GSM153157 3 0.0524 0.5870 0.000 0.008 0.988 0.004
#> GSM153158 3 0.6561 0.2754 0.000 0.092 0.564 0.344
#> GSM153159 3 0.0524 0.5870 0.000 0.008 0.988 0.004
#> GSM153160 3 0.6443 0.2710 0.000 0.076 0.548 0.376
#> GSM153161 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM153162 2 0.7426 -0.5373 0.000 0.452 0.172 0.376
#> GSM153163 3 0.6554 0.2563 0.000 0.084 0.540 0.376
#> GSM153164 2 0.7668 -0.5686 0.000 0.432 0.220 0.348
#> GSM153165 3 0.7098 0.1228 0.000 0.132 0.492 0.376
#> GSM153166 2 0.6658 -0.3738 0.000 0.532 0.092 0.376
#> GSM153167 2 0.4776 -0.1496 0.000 0.624 0.000 0.376
#> GSM153168 3 0.0336 0.5874 0.000 0.008 0.992 0.000
#> GSM153169 3 0.6500 0.2643 0.000 0.080 0.544 0.376
#> GSM153170 4 0.7866 0.3819 0.000 0.276 0.348 0.376
#> GSM153171 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM153172 2 0.4761 -0.1420 0.000 0.628 0.000 0.372
#> GSM153173 3 0.6894 0.1872 0.000 0.112 0.512 0.376
#> GSM153174 2 0.4776 -0.1496 0.000 0.624 0.000 0.376
#> GSM153175 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM153176 4 0.6648 -0.1649 0.000 0.248 0.140 0.612
#> GSM153177 2 0.6708 -0.3829 0.000 0.528 0.096 0.376
#> GSM152931 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM152932 2 0.4761 -0.1420 0.000 0.628 0.000 0.372
#> GSM152933 2 0.6123 -0.2850 0.000 0.572 0.056 0.372
#> GSM152934 2 0.4804 0.4534 0.000 0.616 0.000 0.384
#> GSM152935 4 0.7700 0.4779 0.000 0.384 0.220 0.396
#> GSM152936 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM152937 4 0.7684 0.2085 0.000 0.216 0.388 0.396
#> GSM152938 4 0.7716 0.2350 0.000 0.224 0.380 0.396
#> GSM152939 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM152940 2 0.4948 0.4622 0.000 0.560 0.000 0.440
#> GSM152941 1 0.2593 0.9297 0.892 0.000 0.004 0.104
#> GSM152942 3 0.7448 -0.1114 0.000 0.172 0.428 0.400
#> GSM152943 2 0.4277 0.4430 0.000 0.720 0.000 0.280
#> GSM152944 3 0.6894 0.1872 0.000 0.112 0.512 0.376
#> GSM152945 2 0.1109 0.4173 0.000 0.968 0.004 0.028
#> GSM152946 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM152947 2 0.4948 0.4622 0.000 0.560 0.000 0.440
#> GSM152948 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM152949 4 0.7878 0.4849 0.000 0.340 0.284 0.376
#> GSM152950 4 0.7851 0.4938 0.000 0.356 0.268 0.376
#> GSM152951 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM152952 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM152953 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM152954 2 0.4941 0.4645 0.000 0.564 0.000 0.436
#> GSM152955 2 0.6637 0.0041 0.000 0.540 0.368 0.092
#> GSM152956 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM152957 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM152958 2 0.4948 0.4622 0.000 0.560 0.000 0.440
#> GSM152959 2 0.4941 0.4645 0.000 0.564 0.000 0.436
#> GSM152960 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM152961 2 0.4948 0.4622 0.000 0.560 0.000 0.440
#> GSM152962 4 0.7745 0.4919 0.000 0.372 0.232 0.396
#> GSM152963 2 0.0000 0.4319 0.000 1.000 0.000 0.000
#> GSM152964 3 0.2319 0.5565 0.000 0.040 0.924 0.036
#> GSM152965 2 0.4543 -0.0619 0.000 0.676 0.000 0.324
#> GSM152966 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM152967 2 0.3486 0.1804 0.000 0.812 0.000 0.188
#> GSM152968 4 0.7859 0.4921 0.000 0.352 0.272 0.376
#> GSM152969 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM152970 2 0.4948 0.4622 0.000 0.560 0.000 0.440
#> GSM152971 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM152972 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM152973 4 0.3933 -0.0419 0.000 0.200 0.008 0.792
#> GSM152974 2 0.4776 -0.1496 0.000 0.624 0.000 0.376
#> GSM152975 2 0.1022 0.4343 0.000 0.968 0.000 0.032
#> GSM152976 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM152977 2 0.4941 0.4645 0.000 0.564 0.000 0.436
#> GSM152978 2 0.4941 0.4645 0.000 0.564 0.000 0.436
#> GSM152979 3 0.7098 0.1228 0.000 0.132 0.492 0.376
#> GSM152980 2 0.1637 0.4363 0.000 0.940 0.000 0.060
#> GSM152981 3 0.0336 0.5874 0.000 0.008 0.992 0.000
#> GSM152982 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM152983 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM152984 4 0.4916 0.1103 0.000 0.424 0.000 0.576
#> GSM152985 4 0.5781 -0.4455 0.028 0.484 0.000 0.488
#> GSM152986 2 0.4933 0.4662 0.000 0.568 0.000 0.432
#> GSM152987 1 0.2412 0.9403 0.908 0.000 0.008 0.084
#> GSM152988 2 0.5000 0.4271 0.000 0.504 0.000 0.496
#> GSM152989 2 0.5119 0.4594 0.004 0.556 0.000 0.440
#> GSM152990 3 0.7426 -0.0564 0.000 0.172 0.452 0.376
#> GSM152991 3 0.7761 -0.3219 0.000 0.236 0.388 0.376
#> GSM187524 1 0.2342 0.9419 0.912 0.000 0.008 0.080
#> GSM187525 1 0.2412 0.9408 0.908 0.000 0.008 0.084
#> GSM187526 1 0.2342 0.9419 0.912 0.000 0.008 0.080
#> GSM187527 1 0.1716 0.9547 0.936 0.000 0.000 0.064
#> GSM152856 1 0.1716 0.9547 0.936 0.000 0.000 0.064
#> GSM152857 1 0.1716 0.9547 0.936 0.000 0.000 0.064
#> GSM152858 1 0.1824 0.9516 0.936 0.000 0.004 0.060
#> GSM152859 1 0.2675 0.9360 0.892 0.000 0.008 0.100
#> GSM152860 1 0.1824 0.9516 0.936 0.000 0.004 0.060
#> GSM152861 1 0.0469 0.9594 0.988 0.000 0.000 0.012
#> GSM152862 1 0.1824 0.9516 0.936 0.000 0.004 0.060
#> GSM152863 1 0.0188 0.9594 0.996 0.000 0.000 0.004
#> GSM152864 1 0.0336 0.9596 0.992 0.000 0.000 0.008
#> GSM152865 1 0.0336 0.9596 0.992 0.000 0.000 0.008
#> GSM152866 1 0.1716 0.9547 0.936 0.000 0.000 0.064
#> GSM152867 1 0.0336 0.9596 0.992 0.000 0.000 0.008
#> GSM152868 1 0.0336 0.9596 0.992 0.000 0.000 0.008
#> GSM152869 1 0.0336 0.9596 0.992 0.000 0.000 0.008
#> GSM152870 1 0.1824 0.9516 0.936 0.000 0.004 0.060
#> GSM152871 1 0.1824 0.9516 0.936 0.000 0.004 0.060
#> GSM152872 1 0.1824 0.9516 0.936 0.000 0.004 0.060
#> GSM152873 1 0.1716 0.9547 0.936 0.000 0.000 0.064
#> GSM152874 1 0.1716 0.9547 0.936 0.000 0.000 0.064
#> GSM152875 1 0.1716 0.9547 0.936 0.000 0.000 0.064
#> GSM152876 1 0.1716 0.9547 0.936 0.000 0.000 0.064
#> GSM152877 1 0.1716 0.9547 0.936 0.000 0.000 0.064
#> GSM152878 1 0.1716 0.9547 0.936 0.000 0.000 0.064
#> GSM152879 1 0.1716 0.9547 0.936 0.000 0.000 0.064
#> GSM152880 1 0.1716 0.9547 0.936 0.000 0.000 0.064
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.4928 0.6515 0.000 0.660 0.284 0.056 0.000
#> GSM152805 5 0.3752 0.9395 0.000 0.000 0.292 0.000 0.708
#> GSM152806 5 0.3752 0.9395 0.000 0.000 0.292 0.000 0.708
#> GSM152807 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM152808 5 0.3752 0.9395 0.000 0.000 0.292 0.000 0.708
#> GSM152809 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM152810 5 0.4707 0.8867 0.000 0.064 0.228 0.000 0.708
#> GSM152811 5 0.4227 0.9353 0.000 0.016 0.292 0.000 0.692
#> GSM152812 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM152813 2 0.4928 0.6515 0.000 0.660 0.284 0.056 0.000
#> GSM152814 2 0.4887 0.6484 0.000 0.660 0.288 0.052 0.000
#> GSM152815 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM152816 3 0.0880 0.7749 0.000 0.032 0.968 0.000 0.000
#> GSM152817 5 0.3752 0.9395 0.000 0.000 0.292 0.000 0.708
#> GSM152818 5 0.3752 0.9395 0.000 0.000 0.292 0.000 0.708
#> GSM152819 2 0.4367 0.4863 0.000 0.620 0.372 0.000 0.008
#> GSM152820 2 0.4291 0.2674 0.000 0.536 0.464 0.000 0.000
#> GSM152821 2 0.4887 0.6484 0.000 0.660 0.288 0.052 0.000
#> GSM153115 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM153116 5 0.4702 0.7614 0.000 0.016 0.432 0.000 0.552
#> GSM153117 2 0.5889 0.1618 0.000 0.472 0.428 0.000 0.100
#> GSM153118 2 0.4843 0.6448 0.000 0.660 0.292 0.048 0.000
#> GSM153119 5 0.5461 0.8641 0.000 0.096 0.284 0.000 0.620
#> GSM153120 4 0.0798 0.9413 0.000 0.008 0.000 0.976 0.016
#> GSM153121 3 0.2221 0.7860 0.000 0.052 0.912 0.000 0.036
#> GSM153122 5 0.5373 0.8708 0.000 0.092 0.276 0.000 0.632
#> GSM153123 2 0.5188 0.4016 0.000 0.540 0.416 0.044 0.000
#> GSM153124 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM153125 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM153126 3 0.0162 0.7430 0.000 0.000 0.996 0.000 0.004
#> GSM153127 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM153128 3 0.4035 0.6865 0.000 0.156 0.784 0.000 0.060
#> GSM153129 3 0.3961 0.6365 0.000 0.248 0.736 0.016 0.000
#> GSM153130 3 0.0609 0.7164 0.000 0.000 0.980 0.000 0.020
#> GSM153131 3 0.2377 0.7855 0.000 0.128 0.872 0.000 0.000
#> GSM153132 3 0.2852 0.7561 0.000 0.172 0.828 0.000 0.000
#> GSM153133 2 0.4990 0.6027 0.000 0.628 0.324 0.048 0.000
#> GSM153134 3 0.4249 0.5474 0.000 0.296 0.688 0.016 0.000
#> GSM153135 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM153136 4 0.0324 0.9475 0.000 0.004 0.000 0.992 0.004
#> GSM153137 2 0.4370 0.6923 0.000 0.656 0.008 0.332 0.004
#> GSM153138 2 0.4546 0.7109 0.000 0.688 0.020 0.284 0.008
#> GSM153139 3 0.0703 0.7690 0.000 0.024 0.976 0.000 0.000
#> GSM153140 2 0.4928 0.7295 0.000 0.660 0.056 0.284 0.000
#> GSM153141 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM153142 5 0.4173 0.9351 0.000 0.012 0.300 0.000 0.688
#> GSM153143 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM153144 2 0.5293 0.2577 0.000 0.492 0.460 0.048 0.000
#> GSM153145 5 0.3752 0.9395 0.000 0.000 0.292 0.000 0.708
#> GSM153146 2 0.4843 0.6448 0.000 0.660 0.292 0.048 0.000
#> GSM153147 3 0.4378 0.6007 0.000 0.248 0.716 0.036 0.000
#> GSM153148 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM153149 2 0.4843 0.6448 0.000 0.660 0.292 0.048 0.000
#> GSM153150 4 0.0798 0.9413 0.000 0.008 0.000 0.976 0.016
#> GSM153151 3 0.6035 0.4662 0.000 0.324 0.580 0.040 0.056
#> GSM153152 3 0.4132 0.6105 0.000 0.260 0.720 0.020 0.000
#> GSM153153 2 0.4843 0.6448 0.000 0.660 0.292 0.048 0.000
#> GSM153154 3 0.1608 0.7894 0.000 0.072 0.928 0.000 0.000
#> GSM153155 2 0.5074 0.6619 0.000 0.660 0.268 0.072 0.000
#> GSM153156 3 0.1741 0.7823 0.000 0.040 0.936 0.000 0.024
#> GSM153157 5 0.4761 0.8955 0.000 0.028 0.356 0.000 0.616
#> GSM153158 3 0.3197 0.5322 0.000 0.024 0.836 0.000 0.140
#> GSM153159 5 0.4323 0.9174 0.000 0.012 0.332 0.000 0.656
#> GSM153160 3 0.0162 0.7430 0.000 0.000 0.996 0.000 0.004
#> GSM153161 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM153162 3 0.3579 0.6674 0.000 0.240 0.756 0.004 0.000
#> GSM153163 3 0.0162 0.7430 0.000 0.000 0.996 0.000 0.004
#> GSM153164 2 0.4718 0.5344 0.000 0.636 0.340 0.008 0.016
#> GSM153165 3 0.0794 0.7722 0.000 0.028 0.972 0.000 0.000
#> GSM153166 2 0.4687 0.5807 0.000 0.636 0.336 0.028 0.000
#> GSM153167 3 0.5131 0.2490 0.000 0.364 0.588 0.048 0.000
#> GSM153168 5 0.3752 0.9395 0.000 0.000 0.292 0.000 0.708
#> GSM153169 3 0.0324 0.7401 0.000 0.004 0.992 0.000 0.004
#> GSM153170 3 0.2471 0.7809 0.000 0.136 0.864 0.000 0.000
#> GSM153171 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM153172 2 0.4843 0.6448 0.000 0.660 0.292 0.048 0.000
#> GSM153173 3 0.0290 0.7528 0.000 0.008 0.992 0.000 0.000
#> GSM153174 3 0.4665 0.5499 0.000 0.260 0.692 0.048 0.000
#> GSM153175 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM153176 4 0.3878 0.6115 0.000 0.016 0.236 0.748 0.000
#> GSM153177 2 0.4608 0.5792 0.000 0.640 0.336 0.024 0.000
#> GSM152931 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM152932 2 0.4843 0.6448 0.000 0.660 0.292 0.048 0.000
#> GSM152933 2 0.4642 0.6210 0.000 0.660 0.308 0.032 0.000
#> GSM152934 4 0.3102 0.8347 0.000 0.084 0.000 0.860 0.056
#> GSM152935 2 0.5576 0.1222 0.000 0.512 0.424 0.004 0.060
#> GSM152936 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM152937 3 0.4035 0.6865 0.000 0.156 0.784 0.000 0.060
#> GSM152938 3 0.3442 0.7447 0.000 0.104 0.836 0.000 0.060
#> GSM152939 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM152940 4 0.0693 0.9427 0.000 0.008 0.000 0.980 0.012
#> GSM152941 1 0.6072 0.7503 0.688 0.120 0.004 0.084 0.104
#> GSM152942 3 0.1836 0.7773 0.000 0.032 0.932 0.036 0.000
#> GSM152943 4 0.5335 0.4073 0.000 0.300 0.008 0.632 0.060
#> GSM152944 3 0.0162 0.7481 0.000 0.004 0.996 0.000 0.000
#> GSM152945 2 0.5656 0.6283 0.000 0.684 0.048 0.200 0.068
#> GSM152946 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM152947 4 0.0693 0.9427 0.000 0.008 0.000 0.980 0.012
#> GSM152948 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM152949 3 0.2813 0.7595 0.000 0.168 0.832 0.000 0.000
#> GSM152950 3 0.2929 0.7486 0.000 0.180 0.820 0.000 0.000
#> GSM152951 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM152952 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM152953 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM152954 4 0.0290 0.9463 0.000 0.000 0.000 0.992 0.008
#> GSM152955 4 0.8119 -0.0735 0.000 0.324 0.212 0.352 0.112
#> GSM152956 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM152957 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM152958 4 0.0404 0.9455 0.000 0.000 0.000 0.988 0.012
#> GSM152959 4 0.0566 0.9443 0.000 0.004 0.000 0.984 0.012
#> GSM152960 4 0.1018 0.9395 0.000 0.016 0.000 0.968 0.016
#> GSM152961 4 0.0404 0.9455 0.000 0.000 0.000 0.988 0.012
#> GSM152962 3 0.4162 0.7559 0.000 0.176 0.768 0.000 0.056
#> GSM152963 2 0.4456 0.7148 0.000 0.660 0.020 0.320 0.000
#> GSM152964 5 0.6613 0.8112 0.000 0.132 0.256 0.040 0.572
#> GSM152965 2 0.5060 0.6662 0.000 0.704 0.208 0.080 0.008
#> GSM152966 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM152967 2 0.5414 0.7145 0.000 0.660 0.140 0.200 0.000
#> GSM152968 3 0.2929 0.7486 0.000 0.180 0.820 0.000 0.000
#> GSM152969 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM152970 4 0.0566 0.9443 0.000 0.004 0.000 0.984 0.012
#> GSM152971 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM152972 4 0.0324 0.9475 0.000 0.004 0.000 0.992 0.004
#> GSM152973 3 0.4029 0.5245 0.000 0.004 0.680 0.316 0.000
#> GSM152974 2 0.4843 0.6448 0.000 0.660 0.292 0.048 0.000
#> GSM152975 2 0.4663 0.6360 0.000 0.604 0.020 0.376 0.000
#> GSM152976 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM152977 4 0.0404 0.9412 0.000 0.012 0.000 0.988 0.000
#> GSM152978 4 0.0404 0.9455 0.000 0.000 0.000 0.988 0.012
#> GSM152979 3 0.0794 0.7722 0.000 0.028 0.972 0.000 0.000
#> GSM152980 2 0.4610 0.5292 0.000 0.556 0.012 0.432 0.000
#> GSM152981 5 0.4130 0.9371 0.000 0.012 0.292 0.000 0.696
#> GSM152982 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM152983 4 0.0162 0.9478 0.000 0.004 0.000 0.996 0.000
#> GSM152984 3 0.4795 0.6020 0.000 0.072 0.704 0.224 0.000
#> GSM152985 4 0.1267 0.9249 0.004 0.012 0.000 0.960 0.024
#> GSM152986 4 0.0324 0.9475 0.000 0.004 0.000 0.992 0.004
#> GSM152987 1 0.5172 0.7999 0.728 0.132 0.004 0.012 0.124
#> GSM152988 4 0.1571 0.8794 0.000 0.004 0.060 0.936 0.000
#> GSM152989 4 0.0693 0.9422 0.000 0.008 0.000 0.980 0.012
#> GSM152990 3 0.1197 0.7830 0.000 0.048 0.952 0.000 0.000
#> GSM152991 3 0.5080 0.3047 0.000 0.368 0.588 0.000 0.044
#> GSM187524 1 0.4855 0.8142 0.744 0.132 0.004 0.004 0.116
#> GSM187525 1 0.4855 0.8142 0.744 0.132 0.004 0.004 0.116
#> GSM187526 1 0.4580 0.8238 0.768 0.116 0.004 0.004 0.108
#> GSM187527 1 0.2726 0.8828 0.884 0.052 0.000 0.000 0.064
#> GSM152856 1 0.2719 0.8828 0.884 0.048 0.000 0.000 0.068
#> GSM152857 1 0.2928 0.8780 0.872 0.064 0.000 0.000 0.064
#> GSM152858 1 0.3401 0.8619 0.840 0.096 0.000 0.000 0.064
#> GSM152859 1 0.5033 0.8049 0.716 0.156 0.004 0.000 0.124
#> GSM152860 1 0.3401 0.8619 0.840 0.096 0.000 0.000 0.064
#> GSM152861 1 0.0798 0.8904 0.976 0.008 0.000 0.000 0.016
#> GSM152862 1 0.3401 0.8619 0.840 0.096 0.000 0.000 0.064
#> GSM152863 1 0.0671 0.8911 0.980 0.004 0.000 0.000 0.016
#> GSM152864 1 0.0510 0.8910 0.984 0.000 0.000 0.000 0.016
#> GSM152865 1 0.0510 0.8910 0.984 0.000 0.000 0.000 0.016
#> GSM152866 1 0.2719 0.8828 0.884 0.048 0.000 0.000 0.068
#> GSM152867 1 0.0510 0.8910 0.984 0.000 0.000 0.000 0.016
#> GSM152868 1 0.0510 0.8910 0.984 0.000 0.000 0.000 0.016
#> GSM152869 1 0.0510 0.8910 0.984 0.000 0.000 0.000 0.016
#> GSM152870 1 0.3401 0.8619 0.840 0.096 0.000 0.000 0.064
#> GSM152871 1 0.3401 0.8619 0.840 0.096 0.000 0.000 0.064
#> GSM152872 1 0.3401 0.8619 0.840 0.096 0.000 0.000 0.064
#> GSM152873 1 0.2719 0.8828 0.884 0.048 0.000 0.000 0.068
#> GSM152874 1 0.2719 0.8828 0.884 0.048 0.000 0.000 0.068
#> GSM152875 1 0.2726 0.8828 0.884 0.052 0.000 0.000 0.064
#> GSM152876 1 0.2726 0.8828 0.884 0.052 0.000 0.000 0.064
#> GSM152877 1 0.2719 0.8828 0.884 0.048 0.000 0.000 0.068
#> GSM152878 1 0.2719 0.8828 0.884 0.048 0.000 0.000 0.068
#> GSM152879 1 0.2719 0.8828 0.884 0.048 0.000 0.000 0.068
#> GSM152880 1 0.2719 0.8828 0.884 0.048 0.000 0.000 0.068
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.2100 0.8020 0.000 0.884 0.112 0.000 0.000 0.004
#> GSM152805 5 0.2048 0.8473 0.000 0.000 0.120 0.000 0.880 0.000
#> GSM152806 5 0.2048 0.8473 0.000 0.000 0.120 0.000 0.880 0.000
#> GSM152807 2 0.2118 0.8127 0.000 0.888 0.000 0.104 0.000 0.008
#> GSM152808 5 0.2048 0.8473 0.000 0.000 0.120 0.000 0.880 0.000
#> GSM152809 2 0.2118 0.8127 0.000 0.888 0.000 0.104 0.000 0.008
#> GSM152810 5 0.3453 0.7219 0.000 0.000 0.044 0.000 0.792 0.164
#> GSM152811 5 0.2450 0.8401 0.000 0.000 0.116 0.000 0.868 0.016
#> GSM152812 2 0.2006 0.8135 0.000 0.892 0.000 0.104 0.000 0.004
#> GSM152813 2 0.2100 0.8020 0.000 0.884 0.112 0.000 0.000 0.004
#> GSM152814 2 0.2100 0.8020 0.000 0.884 0.112 0.000 0.000 0.004
#> GSM152815 2 0.2006 0.8135 0.000 0.892 0.000 0.104 0.000 0.004
#> GSM152816 3 0.0713 0.8096 0.000 0.028 0.972 0.000 0.000 0.000
#> GSM152817 5 0.2048 0.8473 0.000 0.000 0.120 0.000 0.880 0.000
#> GSM152818 5 0.2048 0.8473 0.000 0.000 0.120 0.000 0.880 0.000
#> GSM152819 2 0.3453 0.7108 0.000 0.788 0.180 0.000 0.004 0.028
#> GSM152820 2 0.4109 0.4222 0.000 0.648 0.328 0.000 0.000 0.024
#> GSM152821 2 0.2070 0.8042 0.000 0.892 0.100 0.000 0.000 0.008
#> GSM153115 4 0.0653 0.9414 0.000 0.004 0.000 0.980 0.004 0.012
#> GSM153116 5 0.5748 0.6129 0.000 0.020 0.240 0.000 0.580 0.160
#> GSM153117 2 0.6096 0.2457 0.000 0.568 0.260 0.000 0.096 0.076
#> GSM153118 2 0.2312 0.7988 0.000 0.876 0.112 0.000 0.000 0.012
#> GSM153119 5 0.5408 0.3481 0.000 0.000 0.116 0.000 0.476 0.408
#> GSM153120 4 0.1900 0.9018 0.000 0.008 0.000 0.916 0.008 0.068
#> GSM153121 3 0.2221 0.8008 0.000 0.032 0.896 0.000 0.000 0.072
#> GSM153122 5 0.5528 0.3991 0.000 0.000 0.144 0.000 0.508 0.348
#> GSM153123 2 0.3990 0.5112 0.000 0.688 0.284 0.000 0.000 0.028
#> GSM153124 4 0.0653 0.9414 0.000 0.004 0.000 0.980 0.004 0.012
#> GSM153125 4 0.0551 0.9425 0.000 0.004 0.000 0.984 0.004 0.008
#> GSM153126 3 0.0767 0.7989 0.000 0.004 0.976 0.000 0.012 0.008
#> GSM153127 2 0.2118 0.8135 0.000 0.888 0.000 0.104 0.000 0.008
#> GSM153128 3 0.5116 0.0992 0.000 0.040 0.472 0.000 0.020 0.468
#> GSM153129 3 0.2869 0.7525 0.000 0.148 0.832 0.000 0.000 0.020
#> GSM153130 3 0.0767 0.8001 0.000 0.008 0.976 0.000 0.012 0.004
#> GSM153131 3 0.1753 0.8053 0.000 0.084 0.912 0.000 0.000 0.004
#> GSM153132 3 0.2842 0.7825 0.000 0.104 0.852 0.000 0.000 0.044
#> GSM153133 2 0.3134 0.7563 0.000 0.820 0.144 0.000 0.000 0.036
#> GSM153134 3 0.3454 0.6640 0.000 0.208 0.768 0.000 0.000 0.024
#> GSM153135 2 0.2118 0.8135 0.000 0.888 0.000 0.104 0.000 0.008
#> GSM153136 4 0.0405 0.9434 0.000 0.004 0.000 0.988 0.000 0.008
#> GSM153137 2 0.2398 0.8045 0.000 0.876 0.000 0.104 0.000 0.020
#> GSM153138 2 0.2937 0.7918 0.000 0.848 0.000 0.096 0.000 0.056
#> GSM153139 3 0.0692 0.8090 0.000 0.020 0.976 0.000 0.000 0.004
#> GSM153140 2 0.2658 0.8179 0.000 0.876 0.036 0.080 0.000 0.008
#> GSM153141 2 0.2118 0.8135 0.000 0.888 0.000 0.104 0.000 0.008
#> GSM153142 5 0.3717 0.8135 0.000 0.000 0.148 0.000 0.780 0.072
#> GSM153143 2 0.2398 0.8095 0.000 0.876 0.000 0.104 0.000 0.020
#> GSM153144 2 0.4224 0.3879 0.000 0.632 0.340 0.000 0.000 0.028
#> GSM153145 5 0.2048 0.8473 0.000 0.000 0.120 0.000 0.880 0.000
#> GSM153146 2 0.2070 0.8042 0.000 0.892 0.100 0.000 0.000 0.008
#> GSM153147 3 0.2831 0.7590 0.000 0.136 0.840 0.000 0.000 0.024
#> GSM153148 2 0.2118 0.8135 0.000 0.888 0.000 0.104 0.000 0.008
#> GSM153149 2 0.2706 0.7923 0.000 0.860 0.104 0.000 0.000 0.036
#> GSM153150 4 0.1333 0.9221 0.000 0.000 0.000 0.944 0.008 0.048
#> GSM153151 3 0.5758 0.0524 0.000 0.176 0.456 0.000 0.000 0.368
#> GSM153152 3 0.3284 0.7209 0.000 0.168 0.800 0.000 0.000 0.032
#> GSM153153 2 0.2212 0.8000 0.000 0.880 0.112 0.000 0.000 0.008
#> GSM153154 3 0.1418 0.8108 0.000 0.032 0.944 0.000 0.000 0.024
#> GSM153155 2 0.2275 0.8076 0.000 0.888 0.096 0.008 0.000 0.008
#> GSM153156 3 0.1498 0.8101 0.000 0.028 0.940 0.000 0.000 0.032
#> GSM153157 5 0.4749 0.7077 0.000 0.004 0.260 0.000 0.656 0.080
#> GSM153158 3 0.4196 0.5985 0.000 0.024 0.772 0.000 0.120 0.084
#> GSM153159 5 0.4586 0.7043 0.000 0.000 0.264 0.000 0.660 0.076
#> GSM153160 3 0.0767 0.7989 0.000 0.004 0.976 0.000 0.012 0.008
#> GSM153161 2 0.2218 0.8123 0.000 0.884 0.000 0.104 0.000 0.012
#> GSM153162 3 0.2790 0.7652 0.000 0.132 0.844 0.000 0.000 0.024
#> GSM153163 3 0.0767 0.8001 0.000 0.008 0.976 0.000 0.012 0.004
#> GSM153164 2 0.4055 0.6855 0.000 0.760 0.164 0.000 0.008 0.068
#> GSM153165 3 0.0547 0.8097 0.000 0.020 0.980 0.000 0.000 0.000
#> GSM153166 2 0.2692 0.7678 0.000 0.840 0.148 0.000 0.000 0.012
#> GSM153167 3 0.4230 0.3361 0.000 0.364 0.612 0.000 0.000 0.024
#> GSM153168 5 0.2048 0.8473 0.000 0.000 0.120 0.000 0.880 0.000
#> GSM153169 3 0.0767 0.8001 0.000 0.008 0.976 0.000 0.012 0.004
#> GSM153170 3 0.1501 0.8066 0.000 0.076 0.924 0.000 0.000 0.000
#> GSM153171 4 0.0653 0.9414 0.000 0.004 0.000 0.980 0.004 0.012
#> GSM153172 2 0.2100 0.8010 0.000 0.884 0.112 0.000 0.000 0.004
#> GSM153173 3 0.0692 0.8090 0.000 0.020 0.976 0.000 0.000 0.004
#> GSM153174 3 0.3025 0.7385 0.000 0.156 0.820 0.000 0.000 0.024
#> GSM153175 4 0.0653 0.9414 0.000 0.004 0.000 0.980 0.004 0.012
#> GSM153176 4 0.2925 0.7452 0.000 0.000 0.148 0.832 0.004 0.016
#> GSM153177 2 0.2988 0.7617 0.000 0.828 0.144 0.000 0.000 0.028
#> GSM152931 4 0.0653 0.9414 0.000 0.004 0.000 0.980 0.004 0.012
#> GSM152932 2 0.2618 0.7921 0.000 0.860 0.116 0.000 0.000 0.024
#> GSM152933 2 0.2357 0.7968 0.000 0.872 0.116 0.000 0.000 0.012
#> GSM152934 4 0.4178 0.3906 0.000 0.020 0.000 0.608 0.000 0.372
#> GSM152935 6 0.5856 0.4788 0.000 0.368 0.196 0.000 0.000 0.436
#> GSM152936 4 0.0291 0.9437 0.000 0.004 0.000 0.992 0.000 0.004
#> GSM152937 3 0.4937 0.1398 0.000 0.028 0.492 0.000 0.020 0.460
#> GSM152938 3 0.4517 0.5243 0.000 0.024 0.664 0.000 0.024 0.288
#> GSM152939 4 0.0893 0.9377 0.000 0.004 0.004 0.972 0.004 0.016
#> GSM152940 4 0.1196 0.9276 0.000 0.000 0.000 0.952 0.008 0.040
#> GSM152941 1 0.7261 0.4416 0.472 0.040 0.000 0.216 0.052 0.220
#> GSM152942 3 0.1680 0.8067 0.000 0.020 0.940 0.024 0.004 0.012
#> GSM152943 4 0.5802 -0.2119 0.000 0.180 0.000 0.420 0.000 0.400
#> GSM152944 3 0.0547 0.8097 0.000 0.020 0.980 0.000 0.000 0.000
#> GSM152945 6 0.5399 0.4606 0.000 0.368 0.020 0.040 0.016 0.556
#> GSM152946 2 0.2775 0.8046 0.000 0.856 0.000 0.104 0.000 0.040
#> GSM152947 4 0.1196 0.9277 0.000 0.000 0.000 0.952 0.008 0.040
#> GSM152948 2 0.2118 0.8127 0.000 0.888 0.000 0.104 0.000 0.008
#> GSM152949 3 0.2432 0.7897 0.000 0.100 0.876 0.000 0.000 0.024
#> GSM152950 3 0.2712 0.7919 0.000 0.088 0.864 0.000 0.000 0.048
#> GSM152951 2 0.2218 0.8123 0.000 0.884 0.000 0.104 0.000 0.012
#> GSM152952 2 0.2218 0.8123 0.000 0.884 0.000 0.104 0.000 0.012
#> GSM152953 2 0.2118 0.8135 0.000 0.888 0.000 0.104 0.000 0.008
#> GSM152954 4 0.0291 0.9423 0.000 0.000 0.000 0.992 0.004 0.004
#> GSM152955 6 0.7340 0.4522 0.000 0.188 0.076 0.220 0.036 0.480
#> GSM152956 2 0.2118 0.8135 0.000 0.888 0.000 0.104 0.000 0.008
#> GSM152957 4 0.0551 0.9425 0.000 0.004 0.000 0.984 0.004 0.008
#> GSM152958 4 0.0508 0.9409 0.000 0.000 0.000 0.984 0.004 0.012
#> GSM152959 4 0.0972 0.9331 0.000 0.000 0.000 0.964 0.008 0.028
#> GSM152960 4 0.1976 0.9034 0.000 0.016 0.000 0.916 0.008 0.060
#> GSM152961 4 0.0405 0.9417 0.000 0.000 0.000 0.988 0.008 0.004
#> GSM152962 3 0.5029 0.3453 0.000 0.080 0.544 0.000 0.000 0.376
#> GSM152963 2 0.2118 0.8135 0.000 0.888 0.000 0.104 0.000 0.008
#> GSM152964 6 0.5781 -0.2282 0.000 0.000 0.096 0.032 0.336 0.536
#> GSM152965 2 0.4528 0.4690 0.000 0.680 0.048 0.012 0.000 0.260
#> GSM152966 4 0.0291 0.9434 0.000 0.004 0.000 0.992 0.000 0.004
#> GSM152967 2 0.3013 0.8147 0.000 0.864 0.044 0.064 0.000 0.028
#> GSM152968 3 0.2301 0.7921 0.000 0.096 0.884 0.000 0.000 0.020
#> GSM152969 4 0.0146 0.9436 0.000 0.004 0.000 0.996 0.000 0.000
#> GSM152970 4 0.0520 0.9432 0.000 0.000 0.000 0.984 0.008 0.008
#> GSM152971 4 0.0146 0.9436 0.000 0.004 0.000 0.996 0.000 0.000
#> GSM152972 4 0.0405 0.9434 0.000 0.004 0.000 0.988 0.000 0.008
#> GSM152973 3 0.3343 0.6445 0.000 0.000 0.796 0.176 0.004 0.024
#> GSM152974 2 0.2798 0.7889 0.000 0.852 0.112 0.000 0.000 0.036
#> GSM152975 2 0.3593 0.6671 0.000 0.764 0.004 0.208 0.000 0.024
#> GSM152976 4 0.0551 0.9425 0.000 0.004 0.000 0.984 0.004 0.008
#> GSM152977 4 0.0260 0.9427 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM152978 4 0.1049 0.9312 0.000 0.000 0.000 0.960 0.008 0.032
#> GSM152979 3 0.0692 0.8090 0.000 0.020 0.976 0.000 0.000 0.004
#> GSM152980 2 0.3766 0.4799 0.000 0.684 0.000 0.304 0.000 0.012
#> GSM152981 5 0.3439 0.8265 0.000 0.000 0.120 0.000 0.808 0.072
#> GSM152982 4 0.0551 0.9425 0.000 0.004 0.000 0.984 0.004 0.008
#> GSM152983 4 0.0405 0.9439 0.000 0.004 0.000 0.988 0.000 0.008
#> GSM152984 3 0.3610 0.7348 0.000 0.036 0.824 0.104 0.004 0.032
#> GSM152985 4 0.1049 0.9312 0.000 0.000 0.000 0.960 0.008 0.032
#> GSM152986 4 0.0291 0.9437 0.000 0.004 0.000 0.992 0.000 0.004
#> GSM152987 1 0.6087 0.6176 0.556 0.040 0.000 0.032 0.056 0.316
#> GSM152988 4 0.1881 0.8895 0.000 0.004 0.052 0.924 0.004 0.016
#> GSM152989 4 0.0405 0.9430 0.000 0.000 0.000 0.988 0.004 0.008
#> GSM152990 3 0.1049 0.8128 0.000 0.032 0.960 0.000 0.000 0.008
#> GSM152991 6 0.7150 0.4156 0.000 0.276 0.312 0.000 0.076 0.336
#> GSM187524 1 0.5173 0.7145 0.656 0.040 0.000 0.004 0.052 0.248
#> GSM187525 1 0.5173 0.7145 0.656 0.040 0.000 0.004 0.052 0.248
#> GSM187526 1 0.5173 0.7145 0.656 0.040 0.000 0.004 0.052 0.248
#> GSM187527 1 0.2764 0.8286 0.872 0.020 0.000 0.000 0.024 0.084
#> GSM152856 1 0.2734 0.8287 0.872 0.020 0.000 0.000 0.020 0.088
#> GSM152857 1 0.2816 0.8271 0.868 0.020 0.000 0.000 0.024 0.088
#> GSM152858 1 0.4335 0.7754 0.752 0.044 0.012 0.000 0.016 0.176
#> GSM152859 1 0.5837 0.6798 0.592 0.076 0.008 0.000 0.048 0.276
#> GSM152860 1 0.4335 0.7754 0.752 0.044 0.012 0.000 0.016 0.176
#> GSM152861 1 0.0951 0.8354 0.968 0.004 0.000 0.000 0.008 0.020
#> GSM152862 1 0.4335 0.7754 0.752 0.044 0.012 0.000 0.016 0.176
#> GSM152863 1 0.0767 0.8369 0.976 0.004 0.000 0.000 0.012 0.008
#> GSM152864 1 0.0665 0.8368 0.980 0.004 0.000 0.000 0.008 0.008
#> GSM152865 1 0.0665 0.8368 0.980 0.004 0.000 0.000 0.008 0.008
#> GSM152866 1 0.2734 0.8287 0.872 0.020 0.000 0.000 0.020 0.088
#> GSM152867 1 0.0665 0.8368 0.980 0.004 0.000 0.000 0.008 0.008
#> GSM152868 1 0.0665 0.8368 0.980 0.004 0.000 0.000 0.008 0.008
#> GSM152869 1 0.0665 0.8368 0.980 0.004 0.000 0.000 0.008 0.008
#> GSM152870 1 0.4335 0.7754 0.752 0.044 0.012 0.000 0.016 0.176
#> GSM152871 1 0.4335 0.7754 0.752 0.044 0.012 0.000 0.016 0.176
#> GSM152872 1 0.4335 0.7754 0.752 0.044 0.012 0.000 0.016 0.176
#> GSM152873 1 0.2734 0.8287 0.872 0.020 0.000 0.000 0.020 0.088
#> GSM152874 1 0.2734 0.8287 0.872 0.020 0.000 0.000 0.020 0.088
#> GSM152875 1 0.2764 0.8286 0.872 0.020 0.000 0.000 0.024 0.084
#> GSM152876 1 0.2764 0.8286 0.872 0.020 0.000 0.000 0.024 0.084
#> GSM152877 1 0.2734 0.8287 0.872 0.020 0.000 0.000 0.020 0.088
#> GSM152878 1 0.2734 0.8287 0.872 0.020 0.000 0.000 0.020 0.088
#> GSM152879 1 0.2734 0.8287 0.872 0.020 0.000 0.000 0.020 0.088
#> GSM152880 1 0.2734 0.8287 0.872 0.020 0.000 0.000 0.020 0.088
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> SD:kmeans 171 4.03e-27 2
#> SD:kmeans 167 3.00e-28 3
#> SD:kmeans 48 5.27e-09 4
#> SD:kmeans 160 2.75e-30 5
#> SD:kmeans 151 5.91e-31 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "skmeans"]
# you can also extract it by
# res = res_list["SD:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.968 0.987 0.4817 0.518 0.518
#> 3 3 0.833 0.873 0.945 0.3888 0.772 0.577
#> 4 4 0.884 0.878 0.936 0.1104 0.906 0.724
#> 5 5 0.777 0.796 0.874 0.0727 0.907 0.663
#> 6 6 0.760 0.680 0.820 0.0365 0.990 0.949
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.990 0.000 1.000
#> GSM152805 2 0.0000 0.990 0.000 1.000
#> GSM152806 2 0.0000 0.990 0.000 1.000
#> GSM152807 2 0.0000 0.990 0.000 1.000
#> GSM152808 2 0.0000 0.990 0.000 1.000
#> GSM152809 2 0.0000 0.990 0.000 1.000
#> GSM152810 1 0.0000 0.981 1.000 0.000
#> GSM152811 2 0.0000 0.990 0.000 1.000
#> GSM152812 2 0.0000 0.990 0.000 1.000
#> GSM152813 2 0.0000 0.990 0.000 1.000
#> GSM152814 2 0.0000 0.990 0.000 1.000
#> GSM152815 2 0.0000 0.990 0.000 1.000
#> GSM152816 2 0.0000 0.990 0.000 1.000
#> GSM152817 2 0.0000 0.990 0.000 1.000
#> GSM152818 2 0.0000 0.990 0.000 1.000
#> GSM152819 2 0.0000 0.990 0.000 1.000
#> GSM152820 2 0.0000 0.990 0.000 1.000
#> GSM152821 2 0.0000 0.990 0.000 1.000
#> GSM153115 1 0.0000 0.981 1.000 0.000
#> GSM153116 2 0.0000 0.990 0.000 1.000
#> GSM153117 2 0.0000 0.990 0.000 1.000
#> GSM153118 2 0.0000 0.990 0.000 1.000
#> GSM153119 2 0.0000 0.990 0.000 1.000
#> GSM153120 1 0.0000 0.981 1.000 0.000
#> GSM153121 2 0.0000 0.990 0.000 1.000
#> GSM153122 2 0.0000 0.990 0.000 1.000
#> GSM153123 2 0.0000 0.990 0.000 1.000
#> GSM153124 2 0.7376 0.732 0.208 0.792
#> GSM153125 1 0.0000 0.981 1.000 0.000
#> GSM153126 2 0.0000 0.990 0.000 1.000
#> GSM153127 2 0.0000 0.990 0.000 1.000
#> GSM153128 2 0.0000 0.990 0.000 1.000
#> GSM153129 2 0.0000 0.990 0.000 1.000
#> GSM153130 2 0.0000 0.990 0.000 1.000
#> GSM153131 2 0.0000 0.990 0.000 1.000
#> GSM153132 2 0.0000 0.990 0.000 1.000
#> GSM153133 2 0.0000 0.990 0.000 1.000
#> GSM153134 2 0.0000 0.990 0.000 1.000
#> GSM153135 2 0.0000 0.990 0.000 1.000
#> GSM153136 1 0.0000 0.981 1.000 0.000
#> GSM153137 1 0.8267 0.654 0.740 0.260
#> GSM153138 2 0.0000 0.990 0.000 1.000
#> GSM153139 2 0.0000 0.990 0.000 1.000
#> GSM153140 2 0.0000 0.990 0.000 1.000
#> GSM153141 2 0.0000 0.990 0.000 1.000
#> GSM153142 2 0.0000 0.990 0.000 1.000
#> GSM153143 2 0.0000 0.990 0.000 1.000
#> GSM153144 2 0.0000 0.990 0.000 1.000
#> GSM153145 2 0.0000 0.990 0.000 1.000
#> GSM153146 2 0.0000 0.990 0.000 1.000
#> GSM153147 2 0.0000 0.990 0.000 1.000
#> GSM153148 2 0.0000 0.990 0.000 1.000
#> GSM153149 2 0.0000 0.990 0.000 1.000
#> GSM153150 1 0.0000 0.981 1.000 0.000
#> GSM153151 2 0.0000 0.990 0.000 1.000
#> GSM153152 2 0.0000 0.990 0.000 1.000
#> GSM153153 2 0.0000 0.990 0.000 1.000
#> GSM153154 2 0.0000 0.990 0.000 1.000
#> GSM153155 2 0.0000 0.990 0.000 1.000
#> GSM153156 2 0.0000 0.990 0.000 1.000
#> GSM153157 2 0.0000 0.990 0.000 1.000
#> GSM153158 2 0.0000 0.990 0.000 1.000
#> GSM153159 2 0.0000 0.990 0.000 1.000
#> GSM153160 2 0.0000 0.990 0.000 1.000
#> GSM153161 2 0.0000 0.990 0.000 1.000
#> GSM153162 2 0.0000 0.990 0.000 1.000
#> GSM153163 2 0.0000 0.990 0.000 1.000
#> GSM153164 2 0.0000 0.990 0.000 1.000
#> GSM153165 2 0.0000 0.990 0.000 1.000
#> GSM153166 2 0.0000 0.990 0.000 1.000
#> GSM153167 2 0.0000 0.990 0.000 1.000
#> GSM153168 2 0.0000 0.990 0.000 1.000
#> GSM153169 2 0.0000 0.990 0.000 1.000
#> GSM153170 2 0.0000 0.990 0.000 1.000
#> GSM153171 1 0.0000 0.981 1.000 0.000
#> GSM153172 2 0.0000 0.990 0.000 1.000
#> GSM153173 2 0.0000 0.990 0.000 1.000
#> GSM153174 2 0.0000 0.990 0.000 1.000
#> GSM153175 1 0.0000 0.981 1.000 0.000
#> GSM153176 1 0.0000 0.981 1.000 0.000
#> GSM153177 2 0.0000 0.990 0.000 1.000
#> GSM152931 1 0.0000 0.981 1.000 0.000
#> GSM152932 2 0.0000 0.990 0.000 1.000
#> GSM152933 2 0.0000 0.990 0.000 1.000
#> GSM152934 1 0.7602 0.720 0.780 0.220
#> GSM152935 2 0.0000 0.990 0.000 1.000
#> GSM152936 1 0.0000 0.981 1.000 0.000
#> GSM152937 2 0.0000 0.990 0.000 1.000
#> GSM152938 2 0.0000 0.990 0.000 1.000
#> GSM152939 1 0.0376 0.978 0.996 0.004
#> GSM152940 1 0.0000 0.981 1.000 0.000
#> GSM152941 1 0.0000 0.981 1.000 0.000
#> GSM152942 2 0.0000 0.990 0.000 1.000
#> GSM152943 1 0.8386 0.639 0.732 0.268
#> GSM152944 2 0.0000 0.990 0.000 1.000
#> GSM152945 2 0.0000 0.990 0.000 1.000
#> GSM152946 2 0.0000 0.990 0.000 1.000
#> GSM152947 1 0.0000 0.981 1.000 0.000
#> GSM152948 2 0.0000 0.990 0.000 1.000
#> GSM152949 2 0.0000 0.990 0.000 1.000
#> GSM152950 2 0.0000 0.990 0.000 1.000
#> GSM152951 2 0.0000 0.990 0.000 1.000
#> GSM152952 2 0.0000 0.990 0.000 1.000
#> GSM152953 2 0.0000 0.990 0.000 1.000
#> GSM152954 1 0.0000 0.981 1.000 0.000
#> GSM152955 2 0.0000 0.990 0.000 1.000
#> GSM152956 2 0.0000 0.990 0.000 1.000
#> GSM152957 1 0.0000 0.981 1.000 0.000
#> GSM152958 1 0.0000 0.981 1.000 0.000
#> GSM152959 1 0.0000 0.981 1.000 0.000
#> GSM152960 1 0.0000 0.981 1.000 0.000
#> GSM152961 1 0.0000 0.981 1.000 0.000
#> GSM152962 2 0.0000 0.990 0.000 1.000
#> GSM152963 2 0.0000 0.990 0.000 1.000
#> GSM152964 2 0.9833 0.238 0.424 0.576
#> GSM152965 2 0.0000 0.990 0.000 1.000
#> GSM152966 1 0.0000 0.981 1.000 0.000
#> GSM152967 2 0.0000 0.990 0.000 1.000
#> GSM152968 2 0.0000 0.990 0.000 1.000
#> GSM152969 1 0.0000 0.981 1.000 0.000
#> GSM152970 1 0.0000 0.981 1.000 0.000
#> GSM152971 1 0.0000 0.981 1.000 0.000
#> GSM152972 1 0.0000 0.981 1.000 0.000
#> GSM152973 2 0.9044 0.524 0.320 0.680
#> GSM152974 2 0.0000 0.990 0.000 1.000
#> GSM152975 2 0.0000 0.990 0.000 1.000
#> GSM152976 1 0.0000 0.981 1.000 0.000
#> GSM152977 1 0.0000 0.981 1.000 0.000
#> GSM152978 1 0.0000 0.981 1.000 0.000
#> GSM152979 2 0.0000 0.990 0.000 1.000
#> GSM152980 2 0.0000 0.990 0.000 1.000
#> GSM152981 2 0.0000 0.990 0.000 1.000
#> GSM152982 1 0.0000 0.981 1.000 0.000
#> GSM152983 1 0.0000 0.981 1.000 0.000
#> GSM152984 2 0.0000 0.990 0.000 1.000
#> GSM152985 1 0.0000 0.981 1.000 0.000
#> GSM152986 1 0.0000 0.981 1.000 0.000
#> GSM152987 1 0.0000 0.981 1.000 0.000
#> GSM152988 1 0.9970 0.113 0.532 0.468
#> GSM152989 1 0.0000 0.981 1.000 0.000
#> GSM152990 2 0.0000 0.990 0.000 1.000
#> GSM152991 2 0.0000 0.990 0.000 1.000
#> GSM187524 1 0.0000 0.981 1.000 0.000
#> GSM187525 1 0.0000 0.981 1.000 0.000
#> GSM187526 1 0.0000 0.981 1.000 0.000
#> GSM187527 1 0.0000 0.981 1.000 0.000
#> GSM152856 1 0.0000 0.981 1.000 0.000
#> GSM152857 1 0.0000 0.981 1.000 0.000
#> GSM152858 1 0.0000 0.981 1.000 0.000
#> GSM152859 1 0.0000 0.981 1.000 0.000
#> GSM152860 1 0.0000 0.981 1.000 0.000
#> GSM152861 1 0.0000 0.981 1.000 0.000
#> GSM152862 1 0.0000 0.981 1.000 0.000
#> GSM152863 1 0.0000 0.981 1.000 0.000
#> GSM152864 1 0.0000 0.981 1.000 0.000
#> GSM152865 1 0.0000 0.981 1.000 0.000
#> GSM152866 1 0.0000 0.981 1.000 0.000
#> GSM152867 1 0.0000 0.981 1.000 0.000
#> GSM152868 1 0.0000 0.981 1.000 0.000
#> GSM152869 1 0.0000 0.981 1.000 0.000
#> GSM152870 1 0.0000 0.981 1.000 0.000
#> GSM152871 1 0.0000 0.981 1.000 0.000
#> GSM152872 1 0.0000 0.981 1.000 0.000
#> GSM152873 1 0.0000 0.981 1.000 0.000
#> GSM152874 1 0.0000 0.981 1.000 0.000
#> GSM152875 1 0.0000 0.981 1.000 0.000
#> GSM152876 1 0.0000 0.981 1.000 0.000
#> GSM152877 1 0.0000 0.981 1.000 0.000
#> GSM152878 1 0.0000 0.981 1.000 0.000
#> GSM152879 1 0.0000 0.981 1.000 0.000
#> GSM152880 1 0.0000 0.981 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152805 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152806 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152807 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152808 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152809 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152810 3 0.0747 0.9357 0.016 0.000 0.984
#> GSM152811 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152812 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152813 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152814 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152815 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152816 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152817 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152818 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152819 3 0.6026 0.4218 0.000 0.376 0.624
#> GSM152820 3 0.4654 0.7400 0.000 0.208 0.792
#> GSM152821 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM153115 1 0.6079 0.4447 0.612 0.388 0.000
#> GSM153116 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153117 3 0.4452 0.7574 0.000 0.192 0.808
#> GSM153118 2 0.0424 0.9420 0.000 0.992 0.008
#> GSM153119 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153120 1 0.0237 0.9295 0.996 0.004 0.000
#> GSM153121 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153122 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153123 2 0.0592 0.9397 0.000 0.988 0.012
#> GSM153124 2 0.0424 0.9399 0.008 0.992 0.000
#> GSM153125 2 0.6168 0.1979 0.412 0.588 0.000
#> GSM153126 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153127 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM153128 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153129 3 0.6309 0.0205 0.000 0.496 0.504
#> GSM153130 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153131 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153132 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153133 2 0.0424 0.9420 0.000 0.992 0.008
#> GSM153134 2 0.3879 0.7988 0.000 0.848 0.152
#> GSM153135 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM153136 1 0.3619 0.8355 0.864 0.136 0.000
#> GSM153137 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM153138 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM153139 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153140 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM153141 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM153142 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153143 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM153144 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM153145 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153146 2 0.0237 0.9438 0.000 0.996 0.004
#> GSM153147 3 0.4452 0.7602 0.000 0.192 0.808
#> GSM153148 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM153149 2 0.1163 0.9286 0.000 0.972 0.028
#> GSM153150 1 0.0237 0.9295 0.996 0.004 0.000
#> GSM153151 3 0.5016 0.6953 0.000 0.240 0.760
#> GSM153152 2 0.6111 0.3248 0.000 0.604 0.396
#> GSM153153 2 0.0237 0.9438 0.000 0.996 0.004
#> GSM153154 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153155 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM153156 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153157 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153158 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153159 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153160 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153161 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM153162 3 0.5216 0.6517 0.000 0.260 0.740
#> GSM153163 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153164 2 0.6267 0.1469 0.000 0.548 0.452
#> GSM153165 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153166 2 0.1163 0.9283 0.000 0.972 0.028
#> GSM153167 2 0.1643 0.9151 0.000 0.956 0.044
#> GSM153168 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153169 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153170 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153171 1 0.1411 0.9122 0.964 0.036 0.000
#> GSM153172 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM153173 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM153174 2 0.3551 0.8234 0.000 0.868 0.132
#> GSM153175 1 0.4887 0.7313 0.772 0.228 0.000
#> GSM153176 3 0.5926 0.4277 0.356 0.000 0.644
#> GSM153177 2 0.1163 0.9286 0.000 0.972 0.028
#> GSM152931 1 0.6154 0.3957 0.592 0.408 0.000
#> GSM152932 2 0.0592 0.9398 0.000 0.988 0.012
#> GSM152933 2 0.1860 0.9075 0.000 0.948 0.052
#> GSM152934 1 0.8925 0.4106 0.564 0.256 0.180
#> GSM152935 3 0.0747 0.9367 0.000 0.016 0.984
#> GSM152936 1 0.4062 0.8116 0.836 0.164 0.000
#> GSM152937 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152938 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152939 1 0.6307 0.1517 0.512 0.488 0.000
#> GSM152940 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152941 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152942 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152943 2 0.5591 0.5253 0.304 0.696 0.000
#> GSM152944 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152945 3 0.5465 0.6146 0.000 0.288 0.712
#> GSM152946 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152947 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152948 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152949 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152950 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152951 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152952 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152953 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152954 1 0.0592 0.9256 0.988 0.012 0.000
#> GSM152955 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152956 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152957 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152958 1 0.0592 0.9256 0.988 0.012 0.000
#> GSM152959 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152960 1 0.5397 0.6268 0.720 0.280 0.000
#> GSM152961 1 0.0237 0.9295 0.996 0.004 0.000
#> GSM152962 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152963 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152964 3 0.0237 0.9451 0.004 0.000 0.996
#> GSM152965 2 0.0747 0.9376 0.000 0.984 0.016
#> GSM152966 1 0.6062 0.4541 0.616 0.384 0.000
#> GSM152967 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152968 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152969 1 0.5397 0.6560 0.720 0.280 0.000
#> GSM152970 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152971 1 0.4931 0.7264 0.768 0.232 0.000
#> GSM152972 1 0.4062 0.8088 0.836 0.164 0.000
#> GSM152973 3 0.2569 0.9021 0.032 0.032 0.936
#> GSM152974 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152975 2 0.0424 0.9417 0.000 0.992 0.008
#> GSM152976 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152977 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152978 1 0.1529 0.9094 0.960 0.040 0.000
#> GSM152979 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152980 2 0.0000 0.9454 0.000 1.000 0.000
#> GSM152981 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152982 1 0.5000 0.8191 0.832 0.124 0.044
#> GSM152983 1 0.4178 0.8004 0.828 0.172 0.000
#> GSM152984 3 0.2959 0.8626 0.000 0.100 0.900
#> GSM152985 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152986 1 0.2165 0.8933 0.936 0.064 0.000
#> GSM152987 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152988 2 0.7067 0.2764 0.376 0.596 0.028
#> GSM152989 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152990 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM152991 3 0.0000 0.9481 0.000 0.000 1.000
#> GSM187524 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM187525 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM187526 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM187527 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152856 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152857 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152858 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152859 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152860 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152861 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152862 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152863 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152864 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152866 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152867 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152870 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152871 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152873 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152874 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152875 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152876 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152877 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152878 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152879 1 0.0000 0.9313 1.000 0.000 0.000
#> GSM152880 1 0.0000 0.9313 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM152805 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM152806 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM152807 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM152808 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM152809 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM152810 3 0.3257 0.78681 0.152 0.000 0.844 0.004
#> GSM152811 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM152812 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM152813 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM152814 2 0.0188 0.94491 0.000 0.996 0.000 0.004
#> GSM152815 2 0.0336 0.94505 0.000 0.992 0.000 0.008
#> GSM152816 3 0.1042 0.92273 0.000 0.008 0.972 0.020
#> GSM152817 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM152818 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM152819 3 0.5137 0.18721 0.000 0.452 0.544 0.004
#> GSM152820 3 0.4283 0.66792 0.000 0.256 0.740 0.004
#> GSM152821 2 0.0188 0.94491 0.000 0.996 0.000 0.004
#> GSM153115 4 0.1297 0.90644 0.016 0.020 0.000 0.964
#> GSM153116 3 0.0376 0.92055 0.000 0.004 0.992 0.004
#> GSM153117 3 0.4608 0.59101 0.000 0.304 0.692 0.004
#> GSM153118 2 0.0000 0.94361 0.000 1.000 0.000 0.000
#> GSM153119 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM153120 4 0.4907 0.40358 0.420 0.000 0.000 0.580
#> GSM153121 3 0.1256 0.92160 0.000 0.008 0.964 0.028
#> GSM153122 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM153123 2 0.0779 0.93435 0.000 0.980 0.004 0.016
#> GSM153124 4 0.1118 0.88941 0.000 0.036 0.000 0.964
#> GSM153125 4 0.1284 0.90397 0.012 0.024 0.000 0.964
#> GSM153126 3 0.1356 0.92084 0.000 0.008 0.960 0.032
#> GSM153127 2 0.0336 0.94505 0.000 0.992 0.000 0.008
#> GSM153128 3 0.0000 0.92148 0.000 0.000 1.000 0.000
#> GSM153129 3 0.5881 0.29204 0.000 0.420 0.544 0.036
#> GSM153130 3 0.1256 0.92160 0.000 0.008 0.964 0.028
#> GSM153131 3 0.1356 0.92084 0.000 0.008 0.960 0.032
#> GSM153132 3 0.1297 0.92220 0.000 0.016 0.964 0.020
#> GSM153133 2 0.0376 0.94177 0.000 0.992 0.004 0.004
#> GSM153134 2 0.3958 0.77999 0.000 0.824 0.144 0.032
#> GSM153135 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM153136 4 0.1256 0.90970 0.028 0.008 0.000 0.964
#> GSM153137 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM153138 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM153139 3 0.1256 0.92160 0.000 0.008 0.964 0.028
#> GSM153140 2 0.0707 0.94236 0.000 0.980 0.000 0.020
#> GSM153141 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM153142 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM153143 2 0.0707 0.94145 0.000 0.980 0.000 0.020
#> GSM153144 2 0.0657 0.93830 0.000 0.984 0.004 0.012
#> GSM153145 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM153146 2 0.0188 0.94491 0.000 0.996 0.000 0.004
#> GSM153147 3 0.5021 0.69118 0.000 0.240 0.724 0.036
#> GSM153148 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM153149 2 0.0524 0.93923 0.000 0.988 0.008 0.004
#> GSM153150 4 0.1940 0.89240 0.076 0.000 0.000 0.924
#> GSM153151 3 0.4936 0.57095 0.000 0.316 0.672 0.012
#> GSM153152 2 0.5291 0.45160 0.000 0.652 0.324 0.024
#> GSM153153 2 0.0000 0.94361 0.000 1.000 0.000 0.000
#> GSM153154 3 0.0804 0.92257 0.000 0.012 0.980 0.008
#> GSM153155 2 0.0188 0.94491 0.000 0.996 0.000 0.004
#> GSM153156 3 0.1256 0.92160 0.000 0.008 0.964 0.028
#> GSM153157 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM153158 3 0.0376 0.92055 0.000 0.004 0.992 0.004
#> GSM153159 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM153160 3 0.1356 0.92084 0.000 0.008 0.960 0.032
#> GSM153161 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM153162 3 0.5052 0.68512 0.000 0.244 0.720 0.036
#> GSM153163 3 0.1256 0.92177 0.000 0.008 0.964 0.028
#> GSM153164 2 0.5004 0.32756 0.000 0.604 0.392 0.004
#> GSM153165 3 0.1356 0.92084 0.000 0.008 0.960 0.032
#> GSM153166 2 0.0657 0.93648 0.000 0.984 0.004 0.012
#> GSM153167 2 0.2494 0.88697 0.000 0.916 0.048 0.036
#> GSM153168 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM153169 3 0.1004 0.92251 0.000 0.004 0.972 0.024
#> GSM153170 3 0.1488 0.92005 0.000 0.012 0.956 0.032
#> GSM153171 4 0.1209 0.90904 0.032 0.004 0.000 0.964
#> GSM153172 2 0.0188 0.94491 0.000 0.996 0.000 0.004
#> GSM153173 3 0.1356 0.92084 0.000 0.008 0.960 0.032
#> GSM153174 2 0.3557 0.82337 0.000 0.856 0.108 0.036
#> GSM153175 4 0.0672 0.90307 0.008 0.008 0.000 0.984
#> GSM153176 4 0.4353 0.65999 0.012 0.000 0.232 0.756
#> GSM153177 2 0.0927 0.93273 0.000 0.976 0.016 0.008
#> GSM152931 4 0.1297 0.90838 0.020 0.016 0.000 0.964
#> GSM152932 2 0.0779 0.93601 0.000 0.980 0.004 0.016
#> GSM152933 2 0.0524 0.93880 0.000 0.988 0.008 0.004
#> GSM152934 4 0.6556 0.70729 0.176 0.040 0.092 0.692
#> GSM152935 3 0.2198 0.88238 0.000 0.072 0.920 0.008
#> GSM152936 4 0.1356 0.90928 0.032 0.008 0.000 0.960
#> GSM152937 3 0.0657 0.92253 0.000 0.004 0.984 0.012
#> GSM152938 3 0.1356 0.92084 0.000 0.008 0.960 0.032
#> GSM152939 4 0.0469 0.89876 0.000 0.012 0.000 0.988
#> GSM152940 4 0.2868 0.85141 0.136 0.000 0.000 0.864
#> GSM152941 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152942 3 0.1356 0.92084 0.000 0.008 0.960 0.032
#> GSM152943 2 0.6840 0.18940 0.108 0.520 0.000 0.372
#> GSM152944 3 0.1151 0.92214 0.000 0.008 0.968 0.024
#> GSM152945 3 0.5712 0.44747 0.008 0.348 0.620 0.024
#> GSM152946 2 0.1022 0.93826 0.000 0.968 0.000 0.032
#> GSM152947 4 0.3266 0.82383 0.168 0.000 0.000 0.832
#> GSM152948 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM152949 3 0.1610 0.91933 0.000 0.016 0.952 0.032
#> GSM152950 3 0.1520 0.92023 0.000 0.020 0.956 0.024
#> GSM152951 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM152952 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM152953 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM152954 4 0.1284 0.90936 0.024 0.012 0.000 0.964
#> GSM152955 3 0.0469 0.91827 0.000 0.000 0.988 0.012
#> GSM152956 2 0.0469 0.94519 0.000 0.988 0.000 0.012
#> GSM152957 4 0.2469 0.87310 0.108 0.000 0.000 0.892
#> GSM152958 4 0.1209 0.90904 0.032 0.004 0.000 0.964
#> GSM152959 4 0.4564 0.60660 0.328 0.000 0.000 0.672
#> GSM152960 4 0.3796 0.85262 0.096 0.056 0.000 0.848
#> GSM152961 4 0.1302 0.90501 0.044 0.000 0.000 0.956
#> GSM152962 3 0.1297 0.92110 0.000 0.016 0.964 0.020
#> GSM152963 2 0.0336 0.94505 0.000 0.992 0.000 0.008
#> GSM152964 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM152965 2 0.0376 0.94408 0.000 0.992 0.004 0.004
#> GSM152966 4 0.1297 0.90840 0.020 0.016 0.000 0.964
#> GSM152967 2 0.0469 0.94371 0.000 0.988 0.000 0.012
#> GSM152968 3 0.1833 0.91561 0.000 0.024 0.944 0.032
#> GSM152969 4 0.1297 0.90840 0.020 0.016 0.000 0.964
#> GSM152970 1 0.4967 0.00788 0.548 0.000 0.000 0.452
#> GSM152971 4 0.1284 0.90936 0.024 0.012 0.000 0.964
#> GSM152972 4 0.1284 0.90936 0.024 0.012 0.000 0.964
#> GSM152973 4 0.3893 0.70345 0.000 0.008 0.196 0.796
#> GSM152974 2 0.0188 0.94472 0.000 0.996 0.000 0.004
#> GSM152975 2 0.4599 0.70709 0.000 0.760 0.028 0.212
#> GSM152976 4 0.1557 0.90045 0.056 0.000 0.000 0.944
#> GSM152977 4 0.1706 0.90365 0.036 0.000 0.016 0.948
#> GSM152978 4 0.1488 0.90944 0.032 0.012 0.000 0.956
#> GSM152979 3 0.1356 0.92084 0.000 0.008 0.960 0.032
#> GSM152980 2 0.3942 0.69445 0.000 0.764 0.000 0.236
#> GSM152981 3 0.0188 0.92093 0.000 0.000 0.996 0.004
#> GSM152982 4 0.0859 0.89980 0.008 0.008 0.004 0.980
#> GSM152983 4 0.1151 0.90950 0.024 0.008 0.000 0.968
#> GSM152984 3 0.5636 0.55109 0.000 0.044 0.648 0.308
#> GSM152985 4 0.4222 0.69682 0.272 0.000 0.000 0.728
#> GSM152986 4 0.1256 0.90970 0.028 0.008 0.000 0.964
#> GSM152987 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152988 4 0.0376 0.89311 0.000 0.004 0.004 0.992
#> GSM152989 4 0.4925 0.38224 0.428 0.000 0.000 0.572
#> GSM152990 3 0.1356 0.92084 0.000 0.008 0.960 0.032
#> GSM152991 3 0.0376 0.92055 0.000 0.004 0.992 0.004
#> GSM187524 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM187525 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM187526 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM187527 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152856 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152857 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152858 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152859 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152860 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152861 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152862 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152863 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152864 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152866 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152867 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152868 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152870 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152871 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152872 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152873 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152875 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152876 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152877 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152878 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152879 1 0.0000 0.98369 1.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.98369 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.1892 0.8745 0.000 0.916 0.080 0.000 0.004
#> GSM152805 5 0.2471 0.8506 0.000 0.000 0.136 0.000 0.864
#> GSM152806 5 0.2329 0.8562 0.000 0.000 0.124 0.000 0.876
#> GSM152807 2 0.0566 0.8941 0.000 0.984 0.012 0.004 0.000
#> GSM152808 5 0.2280 0.8569 0.000 0.000 0.120 0.000 0.880
#> GSM152809 2 0.0566 0.8941 0.000 0.984 0.012 0.004 0.000
#> GSM152810 5 0.1701 0.8182 0.016 0.000 0.048 0.000 0.936
#> GSM152811 5 0.2280 0.8569 0.000 0.000 0.120 0.000 0.880
#> GSM152812 2 0.0162 0.8937 0.000 0.996 0.000 0.004 0.000
#> GSM152813 2 0.0865 0.8927 0.000 0.972 0.024 0.004 0.000
#> GSM152814 2 0.0703 0.8905 0.000 0.976 0.024 0.000 0.000
#> GSM152815 2 0.0162 0.8937 0.000 0.996 0.000 0.004 0.000
#> GSM152816 3 0.3480 0.7101 0.000 0.000 0.752 0.000 0.248
#> GSM152817 5 0.2280 0.8569 0.000 0.000 0.120 0.000 0.880
#> GSM152818 5 0.2329 0.8562 0.000 0.000 0.124 0.000 0.876
#> GSM152819 5 0.5583 0.6189 0.000 0.208 0.152 0.000 0.640
#> GSM152820 5 0.6609 0.1834 0.000 0.216 0.368 0.000 0.416
#> GSM152821 2 0.0451 0.8937 0.000 0.988 0.008 0.000 0.004
#> GSM153115 4 0.0771 0.8809 0.000 0.004 0.020 0.976 0.000
#> GSM153116 5 0.2674 0.8466 0.000 0.004 0.140 0.000 0.856
#> GSM153117 5 0.6008 0.5237 0.000 0.200 0.216 0.000 0.584
#> GSM153118 2 0.0992 0.8904 0.000 0.968 0.024 0.000 0.008
#> GSM153119 5 0.1965 0.8506 0.000 0.000 0.096 0.000 0.904
#> GSM153120 4 0.5309 0.5547 0.312 0.012 0.000 0.628 0.048
#> GSM153121 3 0.1732 0.7997 0.000 0.000 0.920 0.000 0.080
#> GSM153122 5 0.2377 0.8428 0.000 0.000 0.128 0.000 0.872
#> GSM153123 3 0.4452 -0.0107 0.000 0.496 0.500 0.000 0.004
#> GSM153124 4 0.3584 0.8141 0.000 0.076 0.076 0.840 0.008
#> GSM153125 4 0.0613 0.8819 0.000 0.004 0.008 0.984 0.004
#> GSM153126 3 0.2074 0.7976 0.000 0.000 0.896 0.000 0.104
#> GSM153127 2 0.0162 0.8937 0.000 0.996 0.000 0.004 0.000
#> GSM153128 5 0.4045 0.3257 0.000 0.000 0.356 0.000 0.644
#> GSM153129 3 0.2871 0.7701 0.000 0.088 0.872 0.000 0.040
#> GSM153130 3 0.3074 0.7631 0.000 0.000 0.804 0.000 0.196
#> GSM153131 3 0.3160 0.7743 0.000 0.004 0.808 0.000 0.188
#> GSM153132 3 0.3882 0.7049 0.000 0.020 0.756 0.000 0.224
#> GSM153133 2 0.4574 0.3215 0.000 0.576 0.412 0.000 0.012
#> GSM153134 3 0.3551 0.6590 0.000 0.220 0.772 0.000 0.008
#> GSM153135 2 0.0162 0.8937 0.000 0.996 0.000 0.004 0.000
#> GSM153136 4 0.0613 0.8822 0.000 0.004 0.008 0.984 0.004
#> GSM153137 2 0.1597 0.8813 0.000 0.948 0.008 0.020 0.024
#> GSM153138 2 0.2139 0.8723 0.000 0.920 0.012 0.012 0.056
#> GSM153139 3 0.2929 0.7744 0.000 0.000 0.820 0.000 0.180
#> GSM153140 2 0.2125 0.8809 0.000 0.920 0.052 0.024 0.004
#> GSM153141 2 0.0162 0.8937 0.000 0.996 0.000 0.004 0.000
#> GSM153142 5 0.2329 0.8558 0.000 0.000 0.124 0.000 0.876
#> GSM153143 2 0.2074 0.8676 0.000 0.920 0.016 0.060 0.004
#> GSM153144 3 0.4307 -0.0410 0.000 0.496 0.504 0.000 0.000
#> GSM153145 5 0.2280 0.8569 0.000 0.000 0.120 0.000 0.880
#> GSM153146 2 0.0671 0.8921 0.000 0.980 0.016 0.000 0.004
#> GSM153147 3 0.1830 0.7757 0.000 0.040 0.932 0.000 0.028
#> GSM153148 2 0.0324 0.8935 0.000 0.992 0.004 0.004 0.000
#> GSM153149 2 0.3675 0.7595 0.000 0.788 0.188 0.000 0.024
#> GSM153150 4 0.2906 0.8497 0.060 0.004 0.004 0.884 0.048
#> GSM153151 3 0.5932 0.5619 0.000 0.136 0.612 0.008 0.244
#> GSM153152 3 0.3487 0.6594 0.000 0.212 0.780 0.000 0.008
#> GSM153153 2 0.1331 0.8864 0.000 0.952 0.040 0.000 0.008
#> GSM153154 3 0.3160 0.7435 0.000 0.004 0.808 0.000 0.188
#> GSM153155 2 0.1914 0.8779 0.000 0.924 0.060 0.000 0.016
#> GSM153156 3 0.2891 0.7903 0.000 0.000 0.824 0.000 0.176
#> GSM153157 5 0.2280 0.8568 0.000 0.000 0.120 0.000 0.880
#> GSM153158 5 0.3766 0.7193 0.000 0.004 0.268 0.000 0.728
#> GSM153159 5 0.2648 0.8403 0.000 0.000 0.152 0.000 0.848
#> GSM153160 3 0.2561 0.7902 0.000 0.000 0.856 0.000 0.144
#> GSM153161 2 0.0613 0.8925 0.000 0.984 0.008 0.004 0.004
#> GSM153162 3 0.1830 0.7693 0.000 0.068 0.924 0.000 0.008
#> GSM153163 3 0.3039 0.7663 0.000 0.000 0.808 0.000 0.192
#> GSM153164 5 0.6398 0.4012 0.000 0.300 0.200 0.000 0.500
#> GSM153165 3 0.2179 0.7981 0.000 0.000 0.888 0.000 0.112
#> GSM153166 2 0.4387 0.4773 0.000 0.640 0.348 0.000 0.012
#> GSM153167 3 0.3852 0.6513 0.000 0.220 0.760 0.000 0.020
#> GSM153168 5 0.2230 0.8567 0.000 0.000 0.116 0.000 0.884
#> GSM153169 3 0.3452 0.7136 0.000 0.000 0.756 0.000 0.244
#> GSM153170 3 0.2616 0.8014 0.000 0.020 0.880 0.000 0.100
#> GSM153171 4 0.0798 0.8815 0.000 0.000 0.016 0.976 0.008
#> GSM153172 2 0.0880 0.8894 0.000 0.968 0.032 0.000 0.000
#> GSM153173 3 0.2674 0.7929 0.000 0.004 0.856 0.000 0.140
#> GSM153174 3 0.2648 0.7069 0.000 0.152 0.848 0.000 0.000
#> GSM153175 4 0.1205 0.8771 0.000 0.000 0.040 0.956 0.004
#> GSM153176 4 0.5764 0.4383 0.004 0.000 0.320 0.580 0.096
#> GSM153177 2 0.4014 0.6443 0.000 0.728 0.256 0.000 0.016
#> GSM152931 4 0.0566 0.8811 0.000 0.004 0.012 0.984 0.000
#> GSM152932 2 0.3861 0.6215 0.000 0.712 0.284 0.000 0.004
#> GSM152933 2 0.1740 0.8760 0.000 0.932 0.056 0.000 0.012
#> GSM152934 4 0.7696 0.5389 0.072 0.036 0.132 0.544 0.216
#> GSM152935 5 0.3595 0.7766 0.000 0.044 0.140 0.000 0.816
#> GSM152936 4 0.0833 0.8801 0.000 0.004 0.004 0.976 0.016
#> GSM152937 3 0.4307 0.2450 0.000 0.000 0.500 0.000 0.500
#> GSM152938 3 0.3210 0.7654 0.000 0.000 0.788 0.000 0.212
#> GSM152939 4 0.2017 0.8587 0.000 0.008 0.080 0.912 0.000
#> GSM152940 4 0.2670 0.8486 0.080 0.004 0.000 0.888 0.028
#> GSM152941 1 0.0693 0.9716 0.980 0.000 0.000 0.008 0.012
#> GSM152942 3 0.1571 0.7962 0.000 0.004 0.936 0.000 0.060
#> GSM152943 2 0.7856 0.1476 0.032 0.436 0.036 0.316 0.180
#> GSM152944 3 0.2852 0.7778 0.000 0.000 0.828 0.000 0.172
#> GSM152945 5 0.3482 0.7144 0.000 0.104 0.040 0.012 0.844
#> GSM152946 2 0.4336 0.8048 0.000 0.800 0.108 0.060 0.032
#> GSM152947 4 0.3106 0.8140 0.132 0.000 0.000 0.844 0.024
#> GSM152948 2 0.0451 0.8937 0.000 0.988 0.008 0.004 0.000
#> GSM152949 3 0.1444 0.7934 0.000 0.012 0.948 0.000 0.040
#> GSM152950 3 0.2727 0.7943 0.000 0.016 0.868 0.000 0.116
#> GSM152951 2 0.0671 0.8932 0.000 0.980 0.016 0.004 0.000
#> GSM152952 2 0.0740 0.8921 0.000 0.980 0.008 0.004 0.008
#> GSM152953 2 0.0324 0.8939 0.000 0.992 0.004 0.004 0.000
#> GSM152954 4 0.0771 0.8803 0.000 0.004 0.000 0.976 0.020
#> GSM152955 5 0.1285 0.7979 0.000 0.004 0.036 0.004 0.956
#> GSM152956 2 0.0162 0.8937 0.000 0.996 0.000 0.004 0.000
#> GSM152957 4 0.3246 0.8235 0.120 0.000 0.024 0.848 0.008
#> GSM152958 4 0.0324 0.8812 0.000 0.004 0.000 0.992 0.004
#> GSM152959 4 0.5212 0.3304 0.420 0.000 0.004 0.540 0.036
#> GSM152960 4 0.6375 0.6500 0.068 0.184 0.012 0.656 0.080
#> GSM152961 4 0.0451 0.8815 0.004 0.000 0.000 0.988 0.008
#> GSM152962 3 0.4944 0.4970 0.000 0.032 0.620 0.004 0.344
#> GSM152963 2 0.0486 0.8933 0.000 0.988 0.004 0.004 0.004
#> GSM152964 5 0.0771 0.8050 0.004 0.000 0.020 0.000 0.976
#> GSM152965 2 0.2795 0.8559 0.000 0.880 0.056 0.000 0.064
#> GSM152966 4 0.0486 0.8817 0.000 0.004 0.004 0.988 0.004
#> GSM152967 2 0.3209 0.8366 0.000 0.848 0.120 0.028 0.004
#> GSM152968 3 0.1648 0.7943 0.000 0.020 0.940 0.000 0.040
#> GSM152969 4 0.0486 0.8817 0.000 0.004 0.004 0.988 0.004
#> GSM152970 1 0.4916 0.3611 0.628 0.000 0.016 0.340 0.016
#> GSM152971 4 0.0162 0.8813 0.000 0.004 0.000 0.996 0.000
#> GSM152972 4 0.0324 0.8814 0.000 0.004 0.004 0.992 0.000
#> GSM152973 3 0.3360 0.6632 0.000 0.004 0.816 0.168 0.012
#> GSM152974 2 0.2536 0.8272 0.000 0.868 0.128 0.000 0.004
#> GSM152975 2 0.7177 0.1545 0.000 0.444 0.028 0.216 0.312
#> GSM152976 4 0.1664 0.8780 0.020 0.004 0.020 0.948 0.008
#> GSM152977 4 0.1731 0.8750 0.008 0.000 0.012 0.940 0.040
#> GSM152978 4 0.1074 0.8800 0.012 0.004 0.000 0.968 0.016
#> GSM152979 3 0.2929 0.7731 0.000 0.000 0.820 0.000 0.180
#> GSM152980 2 0.5507 0.6402 0.000 0.688 0.036 0.208 0.068
#> GSM152981 5 0.2230 0.8567 0.000 0.000 0.116 0.000 0.884
#> GSM152982 4 0.1205 0.8764 0.000 0.004 0.040 0.956 0.000
#> GSM152983 4 0.0510 0.8813 0.000 0.000 0.016 0.984 0.000
#> GSM152984 3 0.2582 0.7469 0.000 0.004 0.892 0.080 0.024
#> GSM152985 4 0.4338 0.6370 0.280 0.000 0.000 0.696 0.024
#> GSM152986 4 0.0324 0.8816 0.000 0.004 0.004 0.992 0.000
#> GSM152987 1 0.0703 0.9706 0.976 0.000 0.000 0.000 0.024
#> GSM152988 4 0.3430 0.7298 0.000 0.004 0.220 0.776 0.000
#> GSM152989 4 0.4648 0.2351 0.464 0.000 0.000 0.524 0.012
#> GSM152990 3 0.2536 0.7967 0.000 0.004 0.868 0.000 0.128
#> GSM152991 5 0.2329 0.8472 0.000 0.000 0.124 0.000 0.876
#> GSM187524 1 0.0404 0.9787 0.988 0.000 0.000 0.000 0.012
#> GSM187525 1 0.0510 0.9762 0.984 0.000 0.000 0.000 0.016
#> GSM187526 1 0.0290 0.9801 0.992 0.000 0.000 0.000 0.008
#> GSM187527 1 0.0162 0.9821 0.996 0.000 0.000 0.000 0.004
#> GSM152856 1 0.0162 0.9821 0.996 0.000 0.000 0.000 0.004
#> GSM152857 1 0.0162 0.9821 0.996 0.000 0.000 0.000 0.004
#> GSM152858 1 0.0162 0.9815 0.996 0.000 0.000 0.000 0.004
#> GSM152859 1 0.0404 0.9787 0.988 0.000 0.000 0.000 0.012
#> GSM152860 1 0.0290 0.9805 0.992 0.000 0.000 0.000 0.008
#> GSM152861 1 0.0000 0.9822 1.000 0.000 0.000 0.000 0.000
#> GSM152862 1 0.0290 0.9805 0.992 0.000 0.000 0.000 0.008
#> GSM152863 1 0.0000 0.9822 1.000 0.000 0.000 0.000 0.000
#> GSM152864 1 0.0000 0.9822 1.000 0.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.9822 1.000 0.000 0.000 0.000 0.000
#> GSM152866 1 0.0162 0.9821 0.996 0.000 0.000 0.000 0.004
#> GSM152867 1 0.0000 0.9822 1.000 0.000 0.000 0.000 0.000
#> GSM152868 1 0.0000 0.9822 1.000 0.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.9822 1.000 0.000 0.000 0.000 0.000
#> GSM152870 1 0.0290 0.9805 0.992 0.000 0.000 0.000 0.008
#> GSM152871 1 0.0162 0.9815 0.996 0.000 0.000 0.000 0.004
#> GSM152872 1 0.0290 0.9805 0.992 0.000 0.000 0.000 0.008
#> GSM152873 1 0.0162 0.9821 0.996 0.000 0.000 0.000 0.004
#> GSM152874 1 0.0162 0.9821 0.996 0.000 0.000 0.000 0.004
#> GSM152875 1 0.0162 0.9821 0.996 0.000 0.000 0.000 0.004
#> GSM152876 1 0.0162 0.9821 0.996 0.000 0.000 0.000 0.004
#> GSM152877 1 0.0162 0.9821 0.996 0.000 0.000 0.000 0.004
#> GSM152878 1 0.0162 0.9821 0.996 0.000 0.000 0.000 0.004
#> GSM152879 1 0.0162 0.9821 0.996 0.000 0.000 0.000 0.004
#> GSM152880 1 0.0162 0.9821 0.996 0.000 0.000 0.000 0.004
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.3587 0.7169 0.000 0.792 0.068 0.000 0.000 0.140
#> GSM152805 5 0.1501 0.7924 0.000 0.000 0.076 0.000 0.924 0.000
#> GSM152806 5 0.1075 0.7993 0.000 0.000 0.048 0.000 0.952 0.000
#> GSM152807 2 0.0937 0.7581 0.000 0.960 0.000 0.000 0.000 0.040
#> GSM152808 5 0.1007 0.7986 0.000 0.000 0.044 0.000 0.956 0.000
#> GSM152809 2 0.0937 0.7579 0.000 0.960 0.000 0.000 0.000 0.040
#> GSM152810 5 0.2114 0.7482 0.008 0.000 0.012 0.000 0.904 0.076
#> GSM152811 5 0.1196 0.7962 0.000 0.000 0.040 0.000 0.952 0.008
#> GSM152812 2 0.0865 0.7574 0.000 0.964 0.000 0.000 0.000 0.036
#> GSM152813 2 0.1838 0.7581 0.000 0.916 0.016 0.000 0.000 0.068
#> GSM152814 2 0.1802 0.7599 0.000 0.916 0.012 0.000 0.000 0.072
#> GSM152815 2 0.1075 0.7573 0.000 0.952 0.000 0.000 0.000 0.048
#> GSM152816 3 0.5121 0.5787 0.000 0.008 0.640 0.000 0.232 0.120
#> GSM152817 5 0.1075 0.7993 0.000 0.000 0.048 0.000 0.952 0.000
#> GSM152818 5 0.1075 0.7993 0.000 0.000 0.048 0.000 0.952 0.000
#> GSM152819 5 0.6349 0.4130 0.000 0.156 0.092 0.000 0.572 0.180
#> GSM152820 5 0.7469 0.0530 0.000 0.136 0.272 0.000 0.344 0.248
#> GSM152821 2 0.2306 0.7536 0.000 0.888 0.016 0.000 0.004 0.092
#> GSM153115 4 0.1663 0.7342 0.000 0.000 0.000 0.912 0.000 0.088
#> GSM153116 5 0.2250 0.7854 0.000 0.000 0.064 0.000 0.896 0.040
#> GSM153117 5 0.6289 0.4567 0.000 0.148 0.180 0.000 0.580 0.092
#> GSM153118 2 0.3091 0.7360 0.000 0.824 0.024 0.000 0.004 0.148
#> GSM153119 5 0.1995 0.7821 0.000 0.000 0.036 0.000 0.912 0.052
#> GSM153120 4 0.6504 0.0673 0.252 0.040 0.000 0.504 0.004 0.200
#> GSM153121 3 0.2579 0.7785 0.000 0.000 0.872 0.000 0.040 0.088
#> GSM153122 5 0.2997 0.7552 0.000 0.000 0.096 0.000 0.844 0.060
#> GSM153123 3 0.5912 0.1028 0.000 0.356 0.456 0.000 0.004 0.184
#> GSM153124 4 0.5379 0.4738 0.000 0.088 0.052 0.660 0.000 0.200
#> GSM153125 4 0.1267 0.7428 0.000 0.000 0.000 0.940 0.000 0.060
#> GSM153126 3 0.1616 0.7855 0.000 0.000 0.932 0.000 0.048 0.020
#> GSM153127 2 0.1267 0.7501 0.000 0.940 0.000 0.000 0.000 0.060
#> GSM153128 5 0.5751 0.2259 0.000 0.000 0.256 0.000 0.512 0.232
#> GSM153129 3 0.2604 0.7692 0.000 0.036 0.880 0.000 0.008 0.076
#> GSM153130 3 0.2234 0.7715 0.000 0.000 0.872 0.000 0.124 0.004
#> GSM153131 3 0.3123 0.7689 0.000 0.000 0.836 0.000 0.088 0.076
#> GSM153132 3 0.5333 0.6249 0.000 0.020 0.648 0.000 0.168 0.164
#> GSM153133 2 0.5881 0.2884 0.000 0.500 0.288 0.000 0.004 0.208
#> GSM153134 3 0.4600 0.6038 0.000 0.152 0.708 0.000 0.004 0.136
#> GSM153135 2 0.1267 0.7532 0.000 0.940 0.000 0.000 0.000 0.060
#> GSM153136 4 0.1152 0.7444 0.000 0.000 0.004 0.952 0.000 0.044
#> GSM153137 2 0.3159 0.6576 0.000 0.820 0.000 0.020 0.008 0.152
#> GSM153138 2 0.4597 0.5681 0.000 0.676 0.008 0.008 0.040 0.268
#> GSM153139 3 0.2070 0.7810 0.000 0.000 0.896 0.000 0.092 0.012
#> GSM153140 2 0.4604 0.6692 0.000 0.724 0.076 0.024 0.000 0.176
#> GSM153141 2 0.0547 0.7576 0.000 0.980 0.000 0.000 0.000 0.020
#> GSM153142 5 0.1285 0.7990 0.000 0.000 0.052 0.000 0.944 0.004
#> GSM153143 2 0.3294 0.7104 0.000 0.828 0.008 0.032 0.004 0.128
#> GSM153144 2 0.5720 0.0918 0.000 0.436 0.400 0.000 0.000 0.164
#> GSM153145 5 0.1075 0.7993 0.000 0.000 0.048 0.000 0.952 0.000
#> GSM153146 2 0.2062 0.7541 0.000 0.900 0.008 0.000 0.004 0.088
#> GSM153147 3 0.3232 0.7447 0.000 0.016 0.824 0.000 0.020 0.140
#> GSM153148 2 0.0363 0.7560 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM153149 2 0.5886 0.4490 0.000 0.556 0.172 0.000 0.020 0.252
#> GSM153150 4 0.3680 0.6182 0.072 0.000 0.000 0.784 0.000 0.144
#> GSM153151 3 0.7120 0.2089 0.000 0.120 0.456 0.012 0.116 0.296
#> GSM153152 3 0.5710 0.4846 0.000 0.204 0.600 0.000 0.024 0.172
#> GSM153153 2 0.3453 0.7265 0.000 0.808 0.040 0.000 0.008 0.144
#> GSM153154 3 0.4792 0.6538 0.000 0.004 0.676 0.000 0.208 0.112
#> GSM153155 2 0.4084 0.6954 0.000 0.764 0.060 0.004 0.008 0.164
#> GSM153156 3 0.2595 0.7811 0.000 0.000 0.872 0.000 0.084 0.044
#> GSM153157 5 0.1594 0.7970 0.000 0.000 0.052 0.000 0.932 0.016
#> GSM153158 5 0.4077 0.6821 0.000 0.008 0.180 0.000 0.752 0.060
#> GSM153159 5 0.2112 0.7846 0.000 0.000 0.088 0.000 0.896 0.016
#> GSM153160 3 0.1349 0.7862 0.000 0.000 0.940 0.000 0.056 0.004
#> GSM153161 2 0.1700 0.7356 0.000 0.916 0.000 0.000 0.004 0.080
#> GSM153162 3 0.2070 0.7691 0.000 0.012 0.896 0.000 0.000 0.092
#> GSM153163 3 0.2135 0.7712 0.000 0.000 0.872 0.000 0.128 0.000
#> GSM153164 5 0.6928 0.2848 0.000 0.196 0.136 0.000 0.496 0.172
#> GSM153165 3 0.0790 0.7850 0.000 0.000 0.968 0.000 0.032 0.000
#> GSM153166 2 0.5848 0.3090 0.000 0.468 0.356 0.000 0.004 0.172
#> GSM153167 3 0.5061 0.5585 0.000 0.132 0.656 0.000 0.008 0.204
#> GSM153168 5 0.1219 0.7988 0.000 0.000 0.048 0.000 0.948 0.004
#> GSM153169 3 0.2902 0.7261 0.000 0.000 0.800 0.000 0.196 0.004
#> GSM153170 3 0.1390 0.7879 0.000 0.004 0.948 0.000 0.032 0.016
#> GSM153171 4 0.2146 0.7305 0.000 0.000 0.000 0.880 0.004 0.116
#> GSM153172 2 0.2358 0.7543 0.000 0.876 0.016 0.000 0.000 0.108
#> GSM153173 3 0.1075 0.7859 0.000 0.000 0.952 0.000 0.048 0.000
#> GSM153174 3 0.4026 0.6840 0.000 0.088 0.752 0.000 0.000 0.160
#> GSM153175 4 0.2662 0.7120 0.000 0.000 0.024 0.856 0.000 0.120
#> GSM153176 4 0.7334 -0.0423 0.012 0.000 0.284 0.412 0.088 0.204
#> GSM153177 2 0.6128 0.3752 0.000 0.504 0.284 0.000 0.020 0.192
#> GSM152931 4 0.1501 0.7423 0.000 0.000 0.000 0.924 0.000 0.076
#> GSM152932 2 0.6051 0.3022 0.000 0.460 0.284 0.000 0.004 0.252
#> GSM152933 2 0.4461 0.6744 0.000 0.736 0.076 0.000 0.020 0.168
#> GSM152934 6 0.7707 0.5663 0.048 0.036 0.052 0.252 0.128 0.484
#> GSM152935 5 0.5912 0.4321 0.000 0.052 0.120 0.000 0.592 0.236
#> GSM152936 4 0.2333 0.7206 0.000 0.000 0.004 0.872 0.004 0.120
#> GSM152937 3 0.6213 0.0667 0.004 0.000 0.384 0.000 0.324 0.288
#> GSM152938 3 0.4383 0.6758 0.000 0.000 0.716 0.000 0.108 0.176
#> GSM152939 4 0.3172 0.6798 0.000 0.000 0.036 0.816 0.000 0.148
#> GSM152940 4 0.3643 0.6468 0.076 0.000 0.004 0.808 0.004 0.108
#> GSM152941 1 0.0777 0.9471 0.972 0.000 0.000 0.004 0.000 0.024
#> GSM152942 3 0.1863 0.7798 0.000 0.000 0.920 0.004 0.016 0.060
#> GSM152943 6 0.7557 0.6090 0.020 0.240 0.016 0.160 0.092 0.472
#> GSM152944 3 0.2404 0.7796 0.000 0.000 0.872 0.000 0.112 0.016
#> GSM152945 5 0.5114 0.3484 0.004 0.056 0.000 0.016 0.608 0.316
#> GSM152946 2 0.6134 0.3415 0.000 0.520 0.128 0.020 0.012 0.320
#> GSM152947 4 0.5011 0.4904 0.168 0.000 0.004 0.680 0.008 0.140
#> GSM152948 2 0.1267 0.7560 0.000 0.940 0.000 0.000 0.000 0.060
#> GSM152949 3 0.1858 0.7734 0.000 0.000 0.904 0.000 0.004 0.092
#> GSM152950 3 0.4121 0.7279 0.000 0.012 0.768 0.000 0.092 0.128
#> GSM152951 2 0.1267 0.7582 0.000 0.940 0.000 0.000 0.000 0.060
#> GSM152952 2 0.1556 0.7339 0.000 0.920 0.000 0.000 0.000 0.080
#> GSM152953 2 0.2135 0.7443 0.000 0.872 0.000 0.000 0.000 0.128
#> GSM152954 4 0.1226 0.7418 0.000 0.000 0.004 0.952 0.004 0.040
#> GSM152955 5 0.3128 0.6859 0.000 0.000 0.012 0.008 0.812 0.168
#> GSM152956 2 0.0146 0.7552 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM152957 4 0.5388 0.4836 0.184 0.000 0.004 0.640 0.012 0.160
#> GSM152958 4 0.1152 0.7330 0.000 0.000 0.004 0.952 0.000 0.044
#> GSM152959 4 0.5238 0.1567 0.408 0.000 0.000 0.496 0.000 0.096
#> GSM152960 4 0.6819 -0.2200 0.060 0.244 0.004 0.496 0.004 0.192
#> GSM152961 4 0.0935 0.7403 0.000 0.000 0.004 0.964 0.000 0.032
#> GSM152962 3 0.6249 0.3753 0.000 0.028 0.508 0.000 0.208 0.256
#> GSM152963 2 0.1141 0.7490 0.000 0.948 0.000 0.000 0.000 0.052
#> GSM152964 5 0.2402 0.7029 0.000 0.000 0.004 0.000 0.856 0.140
#> GSM152965 2 0.4724 0.5016 0.000 0.648 0.012 0.000 0.052 0.288
#> GSM152966 4 0.0790 0.7445 0.000 0.000 0.000 0.968 0.000 0.032
#> GSM152967 2 0.4742 0.6362 0.000 0.712 0.084 0.016 0.004 0.184
#> GSM152968 3 0.1983 0.7830 0.000 0.000 0.908 0.000 0.020 0.072
#> GSM152969 4 0.0632 0.7428 0.000 0.000 0.000 0.976 0.000 0.024
#> GSM152970 1 0.5629 0.1317 0.524 0.000 0.004 0.324 0.000 0.148
#> GSM152971 4 0.1007 0.7450 0.000 0.000 0.000 0.956 0.000 0.044
#> GSM152972 4 0.0865 0.7414 0.000 0.000 0.000 0.964 0.000 0.036
#> GSM152973 3 0.4483 0.6051 0.000 0.000 0.732 0.104 0.012 0.152
#> GSM152974 2 0.4304 0.6685 0.000 0.736 0.100 0.000 0.004 0.160
#> GSM152975 2 0.8332 -0.2089 0.000 0.360 0.064 0.176 0.208 0.192
#> GSM152976 4 0.2944 0.7169 0.012 0.000 0.008 0.832 0.000 0.148
#> GSM152977 4 0.3065 0.7069 0.000 0.000 0.004 0.844 0.052 0.100
#> GSM152978 4 0.2312 0.7174 0.008 0.012 0.000 0.896 0.004 0.080
#> GSM152979 3 0.2147 0.7849 0.000 0.000 0.896 0.000 0.084 0.020
#> GSM152980 2 0.7315 0.0829 0.000 0.436 0.056 0.200 0.032 0.276
#> GSM152981 5 0.1408 0.7931 0.000 0.000 0.036 0.000 0.944 0.020
#> GSM152982 4 0.2890 0.7152 0.000 0.000 0.024 0.844 0.004 0.128
#> GSM152983 4 0.1444 0.7439 0.000 0.000 0.000 0.928 0.000 0.072
#> GSM152984 3 0.3151 0.7334 0.000 0.004 0.832 0.028 0.004 0.132
#> GSM152985 4 0.5023 0.3198 0.312 0.000 0.004 0.600 0.000 0.084
#> GSM152986 4 0.0935 0.7452 0.000 0.000 0.004 0.964 0.000 0.032
#> GSM152987 1 0.1204 0.9328 0.944 0.000 0.000 0.000 0.000 0.056
#> GSM152988 4 0.4774 0.5013 0.000 0.000 0.148 0.688 0.004 0.160
#> GSM152989 4 0.5071 0.1440 0.444 0.000 0.004 0.488 0.000 0.064
#> GSM152990 3 0.0972 0.7862 0.000 0.000 0.964 0.000 0.028 0.008
#> GSM152991 5 0.2948 0.7633 0.000 0.000 0.060 0.000 0.848 0.092
#> GSM187524 1 0.0865 0.9447 0.964 0.000 0.000 0.000 0.000 0.036
#> GSM187525 1 0.0865 0.9447 0.964 0.000 0.000 0.000 0.000 0.036
#> GSM187526 1 0.0632 0.9479 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM187527 1 0.1007 0.9457 0.956 0.000 0.000 0.000 0.000 0.044
#> GSM152856 1 0.1007 0.9457 0.956 0.000 0.000 0.000 0.000 0.044
#> GSM152857 1 0.1007 0.9457 0.956 0.000 0.000 0.000 0.000 0.044
#> GSM152858 1 0.0937 0.9435 0.960 0.000 0.000 0.000 0.000 0.040
#> GSM152859 1 0.0937 0.9435 0.960 0.000 0.000 0.000 0.000 0.040
#> GSM152860 1 0.0937 0.9435 0.960 0.000 0.000 0.000 0.000 0.040
#> GSM152861 1 0.0146 0.9508 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM152862 1 0.0937 0.9435 0.960 0.000 0.000 0.000 0.000 0.040
#> GSM152863 1 0.0260 0.9509 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM152864 1 0.0000 0.9512 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.9512 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152866 1 0.1007 0.9457 0.956 0.000 0.000 0.000 0.000 0.044
#> GSM152867 1 0.0146 0.9511 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM152868 1 0.0000 0.9512 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.9512 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152870 1 0.0937 0.9435 0.960 0.000 0.000 0.000 0.000 0.040
#> GSM152871 1 0.0937 0.9435 0.960 0.000 0.000 0.000 0.000 0.040
#> GSM152872 1 0.0937 0.9435 0.960 0.000 0.000 0.000 0.000 0.040
#> GSM152873 1 0.1007 0.9457 0.956 0.000 0.000 0.000 0.000 0.044
#> GSM152874 1 0.1007 0.9457 0.956 0.000 0.000 0.000 0.000 0.044
#> GSM152875 1 0.1007 0.9457 0.956 0.000 0.000 0.000 0.000 0.044
#> GSM152876 1 0.1007 0.9457 0.956 0.000 0.000 0.000 0.000 0.044
#> GSM152877 1 0.1007 0.9457 0.956 0.000 0.000 0.000 0.000 0.044
#> GSM152878 1 0.1007 0.9457 0.956 0.000 0.000 0.000 0.000 0.044
#> GSM152879 1 0.1007 0.9457 0.956 0.000 0.000 0.000 0.000 0.044
#> GSM152880 1 0.1007 0.9457 0.956 0.000 0.000 0.000 0.000 0.044
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> SD:skmeans 169 1.87e-14 2
#> SD:skmeans 159 4.62e-14 3
#> SD:skmeans 162 2.36e-28 4
#> SD:skmeans 156 2.71e-28 5
#> SD:skmeans 140 3.78e-24 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "pam"]
# you can also extract it by
# res = res_list["SD:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.985 0.994 0.3023 0.701 0.701
#> 3 3 0.549 0.743 0.835 0.9786 0.699 0.575
#> 4 4 0.597 0.768 0.809 0.0874 0.951 0.886
#> 5 5 0.659 0.675 0.832 0.0560 0.924 0.809
#> 6 6 0.703 0.761 0.852 0.0363 0.984 0.952
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.994 0.000 1.000
#> GSM152805 2 0.0000 0.994 0.000 1.000
#> GSM152806 2 0.0000 0.994 0.000 1.000
#> GSM152807 2 0.0000 0.994 0.000 1.000
#> GSM152808 2 0.0000 0.994 0.000 1.000
#> GSM152809 2 0.0000 0.994 0.000 1.000
#> GSM152810 2 0.0000 0.994 0.000 1.000
#> GSM152811 2 0.0000 0.994 0.000 1.000
#> GSM152812 2 0.0000 0.994 0.000 1.000
#> GSM152813 2 0.0000 0.994 0.000 1.000
#> GSM152814 2 0.0000 0.994 0.000 1.000
#> GSM152815 2 0.0000 0.994 0.000 1.000
#> GSM152816 2 0.0000 0.994 0.000 1.000
#> GSM152817 2 0.0000 0.994 0.000 1.000
#> GSM152818 2 0.0000 0.994 0.000 1.000
#> GSM152819 2 0.0000 0.994 0.000 1.000
#> GSM152820 2 0.0000 0.994 0.000 1.000
#> GSM152821 2 0.0000 0.994 0.000 1.000
#> GSM153115 2 0.0000 0.994 0.000 1.000
#> GSM153116 2 0.0000 0.994 0.000 1.000
#> GSM153117 2 0.0000 0.994 0.000 1.000
#> GSM153118 2 0.0000 0.994 0.000 1.000
#> GSM153119 2 0.0000 0.994 0.000 1.000
#> GSM153120 2 0.0376 0.991 0.004 0.996
#> GSM153121 2 0.0000 0.994 0.000 1.000
#> GSM153122 2 0.0000 0.994 0.000 1.000
#> GSM153123 2 0.0000 0.994 0.000 1.000
#> GSM153124 2 0.0000 0.994 0.000 1.000
#> GSM153125 2 0.0000 0.994 0.000 1.000
#> GSM153126 2 0.0000 0.994 0.000 1.000
#> GSM153127 2 0.0000 0.994 0.000 1.000
#> GSM153128 2 0.0000 0.994 0.000 1.000
#> GSM153129 2 0.0000 0.994 0.000 1.000
#> GSM153130 2 0.0000 0.994 0.000 1.000
#> GSM153131 2 0.0000 0.994 0.000 1.000
#> GSM153132 2 0.0000 0.994 0.000 1.000
#> GSM153133 2 0.0000 0.994 0.000 1.000
#> GSM153134 2 0.0000 0.994 0.000 1.000
#> GSM153135 2 0.0000 0.994 0.000 1.000
#> GSM153136 2 0.0000 0.994 0.000 1.000
#> GSM153137 2 0.0000 0.994 0.000 1.000
#> GSM153138 2 0.0000 0.994 0.000 1.000
#> GSM153139 2 0.0000 0.994 0.000 1.000
#> GSM153140 2 0.0000 0.994 0.000 1.000
#> GSM153141 2 0.0000 0.994 0.000 1.000
#> GSM153142 2 0.0000 0.994 0.000 1.000
#> GSM153143 2 0.0000 0.994 0.000 1.000
#> GSM153144 2 0.0000 0.994 0.000 1.000
#> GSM153145 2 0.0000 0.994 0.000 1.000
#> GSM153146 2 0.0000 0.994 0.000 1.000
#> GSM153147 2 0.0000 0.994 0.000 1.000
#> GSM153148 2 0.0000 0.994 0.000 1.000
#> GSM153149 2 0.0000 0.994 0.000 1.000
#> GSM153150 2 0.0000 0.994 0.000 1.000
#> GSM153151 2 0.0000 0.994 0.000 1.000
#> GSM153152 2 0.0000 0.994 0.000 1.000
#> GSM153153 2 0.0000 0.994 0.000 1.000
#> GSM153154 2 0.0000 0.994 0.000 1.000
#> GSM153155 2 0.0000 0.994 0.000 1.000
#> GSM153156 2 0.0000 0.994 0.000 1.000
#> GSM153157 2 0.0000 0.994 0.000 1.000
#> GSM153158 2 0.0000 0.994 0.000 1.000
#> GSM153159 2 0.0000 0.994 0.000 1.000
#> GSM153160 2 0.0000 0.994 0.000 1.000
#> GSM153161 2 0.0000 0.994 0.000 1.000
#> GSM153162 2 0.0000 0.994 0.000 1.000
#> GSM153163 2 0.0000 0.994 0.000 1.000
#> GSM153164 2 0.0000 0.994 0.000 1.000
#> GSM153165 2 0.0000 0.994 0.000 1.000
#> GSM153166 2 0.0000 0.994 0.000 1.000
#> GSM153167 2 0.0000 0.994 0.000 1.000
#> GSM153168 2 0.0000 0.994 0.000 1.000
#> GSM153169 2 0.0000 0.994 0.000 1.000
#> GSM153170 2 0.0000 0.994 0.000 1.000
#> GSM153171 2 0.0000 0.994 0.000 1.000
#> GSM153172 2 0.0000 0.994 0.000 1.000
#> GSM153173 2 0.0000 0.994 0.000 1.000
#> GSM153174 2 0.0000 0.994 0.000 1.000
#> GSM153175 2 0.0000 0.994 0.000 1.000
#> GSM153176 2 0.0000 0.994 0.000 1.000
#> GSM153177 2 0.0000 0.994 0.000 1.000
#> GSM152931 2 0.0000 0.994 0.000 1.000
#> GSM152932 2 0.0000 0.994 0.000 1.000
#> GSM152933 2 0.0000 0.994 0.000 1.000
#> GSM152934 2 0.0000 0.994 0.000 1.000
#> GSM152935 2 0.0000 0.994 0.000 1.000
#> GSM152936 2 0.0000 0.994 0.000 1.000
#> GSM152937 2 0.0000 0.994 0.000 1.000
#> GSM152938 2 0.0000 0.994 0.000 1.000
#> GSM152939 2 0.0000 0.994 0.000 1.000
#> GSM152940 2 0.1184 0.979 0.016 0.984
#> GSM152941 1 0.0000 0.988 1.000 0.000
#> GSM152942 2 0.0000 0.994 0.000 1.000
#> GSM152943 2 0.0000 0.994 0.000 1.000
#> GSM152944 2 0.0000 0.994 0.000 1.000
#> GSM152945 2 0.0000 0.994 0.000 1.000
#> GSM152946 2 0.0000 0.994 0.000 1.000
#> GSM152947 2 0.0000 0.994 0.000 1.000
#> GSM152948 2 0.0000 0.994 0.000 1.000
#> GSM152949 2 0.0000 0.994 0.000 1.000
#> GSM152950 2 0.0000 0.994 0.000 1.000
#> GSM152951 2 0.0000 0.994 0.000 1.000
#> GSM152952 2 0.0000 0.994 0.000 1.000
#> GSM152953 2 0.0000 0.994 0.000 1.000
#> GSM152954 2 0.0000 0.994 0.000 1.000
#> GSM152955 2 0.0000 0.994 0.000 1.000
#> GSM152956 2 0.0000 0.994 0.000 1.000
#> GSM152957 2 0.0000 0.994 0.000 1.000
#> GSM152958 2 0.2043 0.963 0.032 0.968
#> GSM152959 2 0.0000 0.994 0.000 1.000
#> GSM152960 2 0.0000 0.994 0.000 1.000
#> GSM152961 2 0.4161 0.905 0.084 0.916
#> GSM152962 2 0.0000 0.994 0.000 1.000
#> GSM152963 2 0.0000 0.994 0.000 1.000
#> GSM152964 2 0.0000 0.994 0.000 1.000
#> GSM152965 2 0.0000 0.994 0.000 1.000
#> GSM152966 2 0.0000 0.994 0.000 1.000
#> GSM152967 2 0.0000 0.994 0.000 1.000
#> GSM152968 2 0.0000 0.994 0.000 1.000
#> GSM152969 2 0.0000 0.994 0.000 1.000
#> GSM152970 2 0.0000 0.994 0.000 1.000
#> GSM152971 2 0.0000 0.994 0.000 1.000
#> GSM152972 2 0.0000 0.994 0.000 1.000
#> GSM152973 2 0.0000 0.994 0.000 1.000
#> GSM152974 2 0.0000 0.994 0.000 1.000
#> GSM152975 2 0.0000 0.994 0.000 1.000
#> GSM152976 2 0.0000 0.994 0.000 1.000
#> GSM152977 2 0.0000 0.994 0.000 1.000
#> GSM152978 2 0.0000 0.994 0.000 1.000
#> GSM152979 2 0.0000 0.994 0.000 1.000
#> GSM152980 2 0.0000 0.994 0.000 1.000
#> GSM152981 2 0.0000 0.994 0.000 1.000
#> GSM152982 2 0.0000 0.994 0.000 1.000
#> GSM152983 2 0.0000 0.994 0.000 1.000
#> GSM152984 2 0.0000 0.994 0.000 1.000
#> GSM152985 1 0.8016 0.678 0.756 0.244
#> GSM152986 2 0.0000 0.994 0.000 1.000
#> GSM152987 1 0.0376 0.985 0.996 0.004
#> GSM152988 2 0.0000 0.994 0.000 1.000
#> GSM152989 2 0.9491 0.410 0.368 0.632
#> GSM152990 2 0.0000 0.994 0.000 1.000
#> GSM152991 2 0.0000 0.994 0.000 1.000
#> GSM187524 1 0.0000 0.988 1.000 0.000
#> GSM187525 1 0.0000 0.988 1.000 0.000
#> GSM187526 1 0.0000 0.988 1.000 0.000
#> GSM187527 1 0.4562 0.891 0.904 0.096
#> GSM152856 1 0.0000 0.988 1.000 0.000
#> GSM152857 2 0.8267 0.646 0.260 0.740
#> GSM152858 1 0.0000 0.988 1.000 0.000
#> GSM152859 1 0.0000 0.988 1.000 0.000
#> GSM152860 1 0.0000 0.988 1.000 0.000
#> GSM152861 1 0.0000 0.988 1.000 0.000
#> GSM152862 1 0.0000 0.988 1.000 0.000
#> GSM152863 1 0.0000 0.988 1.000 0.000
#> GSM152864 1 0.0000 0.988 1.000 0.000
#> GSM152865 1 0.0000 0.988 1.000 0.000
#> GSM152866 1 0.0000 0.988 1.000 0.000
#> GSM152867 1 0.0000 0.988 1.000 0.000
#> GSM152868 1 0.0000 0.988 1.000 0.000
#> GSM152869 1 0.0000 0.988 1.000 0.000
#> GSM152870 1 0.0000 0.988 1.000 0.000
#> GSM152871 1 0.0000 0.988 1.000 0.000
#> GSM152872 1 0.0000 0.988 1.000 0.000
#> GSM152873 1 0.0000 0.988 1.000 0.000
#> GSM152874 1 0.0000 0.988 1.000 0.000
#> GSM152875 1 0.0000 0.988 1.000 0.000
#> GSM152876 1 0.0000 0.988 1.000 0.000
#> GSM152877 1 0.0000 0.988 1.000 0.000
#> GSM152878 1 0.0000 0.988 1.000 0.000
#> GSM152879 1 0.0000 0.988 1.000 0.000
#> GSM152880 1 0.0000 0.988 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 3 0.0237 0.7306 0.000 0.004 0.996
#> GSM152805 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM152806 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM152807 3 0.0237 0.7253 0.000 0.004 0.996
#> GSM152808 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM152809 3 0.5835 -0.2335 0.000 0.340 0.660
#> GSM152810 2 0.4931 0.3559 0.000 0.768 0.232
#> GSM152811 3 0.6111 0.6912 0.000 0.396 0.604
#> GSM152812 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM152813 3 0.0237 0.7306 0.000 0.004 0.996
#> GSM152814 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM152815 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM152816 3 0.5905 0.7132 0.000 0.352 0.648
#> GSM152817 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM152818 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM152819 3 0.1860 0.7426 0.000 0.052 0.948
#> GSM152820 3 0.2165 0.7441 0.000 0.064 0.936
#> GSM152821 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM153115 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM153116 3 0.5254 0.7359 0.000 0.264 0.736
#> GSM153117 3 0.5465 0.7307 0.000 0.288 0.712
#> GSM153118 3 0.1529 0.7405 0.000 0.040 0.960
#> GSM153119 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM153120 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM153121 3 0.6235 0.6480 0.000 0.436 0.564
#> GSM153122 3 0.6062 0.6991 0.000 0.384 0.616
#> GSM153123 3 0.2356 0.7449 0.000 0.072 0.928
#> GSM153124 3 0.1031 0.7033 0.000 0.024 0.976
#> GSM153125 2 0.6062 0.8236 0.000 0.616 0.384
#> GSM153126 2 0.0000 0.5583 0.000 1.000 0.000
#> GSM153127 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM153128 3 0.4654 0.7397 0.000 0.208 0.792
#> GSM153129 3 0.4842 0.7434 0.000 0.224 0.776
#> GSM153130 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM153131 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM153132 3 0.5363 0.7332 0.000 0.276 0.724
#> GSM153133 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM153134 3 0.4654 0.7389 0.000 0.208 0.792
#> GSM153135 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM153136 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM153137 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM153138 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM153139 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM153140 3 0.0747 0.7344 0.000 0.016 0.984
#> GSM153141 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM153142 3 0.5988 0.7067 0.000 0.368 0.632
#> GSM153143 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM153144 3 0.4121 0.4270 0.000 0.168 0.832
#> GSM153145 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM153146 3 0.0424 0.7323 0.000 0.008 0.992
#> GSM153147 2 0.5706 0.5831 0.000 0.680 0.320
#> GSM153148 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM153149 3 0.0237 0.7311 0.000 0.004 0.996
#> GSM153150 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM153151 3 0.5621 0.7254 0.000 0.308 0.692
#> GSM153152 3 0.3192 0.7304 0.000 0.112 0.888
#> GSM153153 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM153154 3 0.5591 0.7276 0.000 0.304 0.696
#> GSM153155 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM153156 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM153157 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM153158 3 0.5560 0.7288 0.000 0.300 0.700
#> GSM153159 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM153160 2 0.5397 -0.0356 0.000 0.720 0.280
#> GSM153161 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM153162 2 0.3192 0.6671 0.000 0.888 0.112
#> GSM153163 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM153164 3 0.1289 0.7387 0.000 0.032 0.968
#> GSM153165 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM153166 3 0.4121 0.7433 0.000 0.168 0.832
#> GSM153167 3 0.1753 0.7423 0.000 0.048 0.952
#> GSM153168 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM153169 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM153170 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM153171 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM153172 3 0.0424 0.7323 0.000 0.008 0.992
#> GSM153173 3 0.6111 0.6912 0.000 0.396 0.604
#> GSM153174 2 0.5905 0.8283 0.000 0.648 0.352
#> GSM153175 2 0.5988 0.8319 0.000 0.632 0.368
#> GSM153176 2 0.1031 0.5849 0.000 0.976 0.024
#> GSM153177 3 0.3340 0.7462 0.000 0.120 0.880
#> GSM152931 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152932 3 0.0237 0.7309 0.000 0.004 0.996
#> GSM152933 3 0.2878 0.7461 0.000 0.096 0.904
#> GSM152934 2 0.5988 0.8324 0.000 0.632 0.368
#> GSM152935 3 0.5098 0.7376 0.000 0.248 0.752
#> GSM152936 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152937 3 0.5859 0.7140 0.000 0.344 0.656
#> GSM152938 3 0.5948 0.6510 0.000 0.360 0.640
#> GSM152939 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152940 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152941 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152942 2 0.0892 0.5793 0.000 0.980 0.020
#> GSM152943 3 0.0424 0.7213 0.000 0.008 0.992
#> GSM152944 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM152945 3 0.0892 0.7366 0.000 0.020 0.980
#> GSM152946 3 0.0237 0.7309 0.000 0.004 0.996
#> GSM152947 2 0.5926 0.8297 0.000 0.644 0.356
#> GSM152948 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM152949 2 0.4555 0.2627 0.000 0.800 0.200
#> GSM152950 2 0.5497 0.6125 0.000 0.708 0.292
#> GSM152951 3 0.0237 0.7254 0.000 0.004 0.996
#> GSM152952 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM152953 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM152954 2 0.6154 0.7999 0.000 0.592 0.408
#> GSM152955 3 0.3879 0.7397 0.000 0.152 0.848
#> GSM152956 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM152957 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152958 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152959 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152960 3 0.4887 0.2416 0.000 0.228 0.772
#> GSM152961 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152962 3 0.4452 0.7465 0.000 0.192 0.808
#> GSM152963 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM152964 3 0.5560 0.7067 0.000 0.300 0.700
#> GSM152965 3 0.0000 0.7290 0.000 0.000 1.000
#> GSM152966 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152967 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152968 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM152969 2 0.6307 0.6823 0.000 0.512 0.488
#> GSM152970 2 0.6062 0.8240 0.000 0.616 0.384
#> GSM152971 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152972 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152973 2 0.1289 0.5923 0.000 0.968 0.032
#> GSM152974 3 0.0237 0.7309 0.000 0.004 0.996
#> GSM152975 3 0.5327 0.0612 0.000 0.272 0.728
#> GSM152976 2 0.5760 0.8170 0.000 0.672 0.328
#> GSM152977 2 0.3752 0.6678 0.000 0.856 0.144
#> GSM152978 3 0.5882 -0.2630 0.000 0.348 0.652
#> GSM152979 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM152980 3 0.0747 0.7344 0.000 0.016 0.984
#> GSM152981 3 0.5988 0.7067 0.000 0.368 0.632
#> GSM152982 2 0.5254 0.7784 0.000 0.736 0.264
#> GSM152983 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152984 2 0.5363 0.7918 0.000 0.724 0.276
#> GSM152985 2 0.8339 0.6943 0.168 0.628 0.204
#> GSM152986 2 0.6008 0.8328 0.000 0.628 0.372
#> GSM152987 1 0.1015 0.9683 0.980 0.012 0.008
#> GSM152988 2 0.4399 0.7282 0.000 0.812 0.188
#> GSM152989 2 0.6912 0.8229 0.028 0.628 0.344
#> GSM152990 3 0.6008 0.7057 0.000 0.372 0.628
#> GSM152991 3 0.4235 0.7373 0.000 0.176 0.824
#> GSM187524 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM187525 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM187526 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM187527 2 0.6962 0.1934 0.412 0.568 0.020
#> GSM152856 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152857 2 0.8508 0.4476 0.232 0.608 0.160
#> GSM152858 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152859 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152860 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152861 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152862 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152863 1 0.0747 0.9727 0.984 0.016 0.000
#> GSM152864 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152866 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152867 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152870 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152871 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152873 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152874 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152875 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152876 1 0.4796 0.7147 0.780 0.220 0.000
#> GSM152877 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152878 1 0.3116 0.8738 0.892 0.108 0.000
#> GSM152879 1 0.0000 0.9862 1.000 0.000 0.000
#> GSM152880 1 0.0000 0.9862 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.2281 0.785 0.000 0.904 0.000 0.096
#> GSM152805 2 0.4776 0.691 0.000 0.624 0.376 0.000
#> GSM152806 2 0.4776 0.691 0.000 0.624 0.376 0.000
#> GSM152807 2 0.2530 0.781 0.000 0.888 0.000 0.112
#> GSM152808 2 0.4776 0.691 0.000 0.624 0.376 0.000
#> GSM152809 2 0.4961 0.115 0.000 0.552 0.000 0.448
#> GSM152810 4 0.7752 0.196 0.000 0.236 0.360 0.404
#> GSM152811 2 0.4950 0.688 0.000 0.620 0.376 0.004
#> GSM152812 2 0.2408 0.784 0.000 0.896 0.000 0.104
#> GSM152813 2 0.2345 0.785 0.000 0.900 0.000 0.100
#> GSM152814 2 0.2408 0.784 0.000 0.896 0.000 0.104
#> GSM152815 2 0.2469 0.782 0.000 0.892 0.000 0.108
#> GSM152816 2 0.3649 0.771 0.000 0.796 0.204 0.000
#> GSM152817 2 0.4776 0.691 0.000 0.624 0.376 0.000
#> GSM152818 2 0.4776 0.691 0.000 0.624 0.376 0.000
#> GSM152819 2 0.2081 0.788 0.000 0.916 0.000 0.084
#> GSM152820 2 0.2563 0.791 0.000 0.908 0.020 0.072
#> GSM152821 2 0.2469 0.782 0.000 0.892 0.000 0.108
#> GSM153115 4 0.2081 0.806 0.000 0.084 0.000 0.916
#> GSM153116 2 0.5136 0.775 0.000 0.728 0.224 0.048
#> GSM153117 2 0.4877 0.781 0.000 0.752 0.204 0.044
#> GSM153118 2 0.2149 0.787 0.000 0.912 0.000 0.088
#> GSM153119 2 0.4483 0.743 0.000 0.712 0.284 0.004
#> GSM153120 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM153121 2 0.5995 0.704 0.000 0.660 0.256 0.084
#> GSM153122 2 0.4744 0.737 0.000 0.704 0.284 0.012
#> GSM153123 2 0.2179 0.791 0.000 0.924 0.012 0.064
#> GSM153124 2 0.4193 0.694 0.000 0.732 0.000 0.268
#> GSM153125 4 0.1118 0.834 0.000 0.036 0.000 0.964
#> GSM153126 4 0.6245 0.558 0.000 0.108 0.244 0.648
#> GSM153127 2 0.2469 0.782 0.000 0.892 0.000 0.108
#> GSM153128 2 0.5288 0.775 0.000 0.720 0.224 0.056
#> GSM153129 2 0.3674 0.792 0.000 0.852 0.104 0.044
#> GSM153130 2 0.4222 0.748 0.000 0.728 0.272 0.000
#> GSM153131 2 0.4164 0.751 0.000 0.736 0.264 0.000
#> GSM153132 2 0.4840 0.769 0.000 0.732 0.240 0.028
#> GSM153133 2 0.2868 0.775 0.000 0.864 0.000 0.136
#> GSM153134 2 0.2313 0.792 0.000 0.924 0.044 0.032
#> GSM153135 2 0.2530 0.782 0.000 0.888 0.000 0.112
#> GSM153136 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM153137 2 0.2469 0.782 0.000 0.892 0.000 0.108
#> GSM153138 2 0.2408 0.784 0.000 0.896 0.000 0.104
#> GSM153139 2 0.4134 0.753 0.000 0.740 0.260 0.000
#> GSM153140 2 0.2081 0.787 0.000 0.916 0.000 0.084
#> GSM153141 2 0.2469 0.782 0.000 0.892 0.000 0.108
#> GSM153142 2 0.5204 0.693 0.000 0.612 0.376 0.012
#> GSM153143 2 0.4222 0.698 0.000 0.728 0.000 0.272
#> GSM153144 2 0.4382 0.566 0.000 0.704 0.000 0.296
#> GSM153145 2 0.4776 0.691 0.000 0.624 0.376 0.000
#> GSM153146 2 0.2281 0.785 0.000 0.904 0.000 0.096
#> GSM153147 4 0.6885 0.511 0.000 0.208 0.196 0.596
#> GSM153148 2 0.2469 0.782 0.000 0.892 0.000 0.108
#> GSM153149 2 0.2408 0.784 0.000 0.896 0.000 0.104
#> GSM153150 4 0.0469 0.845 0.000 0.012 0.000 0.988
#> GSM153151 2 0.4728 0.771 0.000 0.752 0.216 0.032
#> GSM153152 2 0.6265 0.771 0.000 0.656 0.220 0.124
#> GSM153153 2 0.2408 0.784 0.000 0.896 0.000 0.104
#> GSM153154 2 0.5256 0.758 0.000 0.692 0.272 0.036
#> GSM153155 2 0.2469 0.782 0.000 0.892 0.000 0.108
#> GSM153156 2 0.4193 0.749 0.000 0.732 0.268 0.000
#> GSM153157 2 0.4222 0.748 0.000 0.728 0.272 0.000
#> GSM153158 2 0.4939 0.776 0.000 0.740 0.220 0.040
#> GSM153159 2 0.4331 0.741 0.000 0.712 0.288 0.000
#> GSM153160 2 0.7850 0.107 0.000 0.388 0.272 0.340
#> GSM153161 2 0.2469 0.782 0.000 0.892 0.000 0.108
#> GSM153162 4 0.6068 0.625 0.000 0.116 0.208 0.676
#> GSM153163 2 0.4222 0.748 0.000 0.728 0.272 0.000
#> GSM153164 2 0.3497 0.790 0.000 0.860 0.036 0.104
#> GSM153165 2 0.4193 0.749 0.000 0.732 0.268 0.000
#> GSM153166 2 0.1302 0.789 0.000 0.956 0.000 0.044
#> GSM153167 2 0.1978 0.790 0.000 0.928 0.004 0.068
#> GSM153168 2 0.4776 0.691 0.000 0.624 0.376 0.000
#> GSM153169 2 0.4193 0.749 0.000 0.732 0.268 0.000
#> GSM153170 2 0.4222 0.748 0.000 0.728 0.272 0.000
#> GSM153171 4 0.2081 0.805 0.000 0.084 0.000 0.916
#> GSM153172 2 0.2281 0.785 0.000 0.904 0.000 0.096
#> GSM153173 2 0.4882 0.739 0.000 0.708 0.272 0.020
#> GSM153174 4 0.3708 0.754 0.000 0.148 0.020 0.832
#> GSM153175 4 0.0336 0.846 0.000 0.008 0.000 0.992
#> GSM153176 4 0.3245 0.757 0.000 0.100 0.028 0.872
#> GSM153177 2 0.3107 0.795 0.000 0.884 0.036 0.080
#> GSM152931 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM152932 2 0.2530 0.787 0.000 0.896 0.004 0.100
#> GSM152933 2 0.1867 0.789 0.000 0.928 0.000 0.072
#> GSM152934 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM152935 2 0.4756 0.787 0.000 0.772 0.176 0.052
#> GSM152936 4 0.2408 0.792 0.000 0.104 0.000 0.896
#> GSM152937 2 0.5021 0.758 0.000 0.724 0.240 0.036
#> GSM152938 2 0.6075 0.687 0.000 0.684 0.148 0.168
#> GSM152939 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM152940 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM152941 1 0.3024 0.673 0.852 0.000 0.000 0.148
#> GSM152942 4 0.5383 0.653 0.000 0.100 0.160 0.740
#> GSM152943 2 0.4382 0.677 0.000 0.704 0.000 0.296
#> GSM152944 2 0.4222 0.748 0.000 0.728 0.272 0.000
#> GSM152945 2 0.3877 0.790 0.000 0.840 0.048 0.112
#> GSM152946 2 0.2408 0.785 0.000 0.896 0.000 0.104
#> GSM152947 4 0.0188 0.846 0.000 0.004 0.000 0.996
#> GSM152948 2 0.2408 0.784 0.000 0.896 0.000 0.104
#> GSM152949 4 0.7746 0.214 0.000 0.288 0.272 0.440
#> GSM152950 4 0.6797 0.526 0.000 0.160 0.240 0.600
#> GSM152951 2 0.2647 0.779 0.000 0.880 0.000 0.120
#> GSM152952 2 0.2469 0.782 0.000 0.892 0.000 0.108
#> GSM152953 2 0.2408 0.784 0.000 0.896 0.000 0.104
#> GSM152954 4 0.1118 0.834 0.000 0.036 0.000 0.964
#> GSM152955 2 0.5690 0.741 0.000 0.708 0.096 0.196
#> GSM152956 2 0.2469 0.782 0.000 0.892 0.000 0.108
#> GSM152957 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM152958 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM152959 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM152960 4 0.4994 -0.155 0.000 0.480 0.000 0.520
#> GSM152961 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM152962 2 0.5143 0.784 0.000 0.752 0.172 0.076
#> GSM152963 2 0.2469 0.782 0.000 0.892 0.000 0.108
#> GSM152964 2 0.6394 0.732 0.000 0.636 0.244 0.120
#> GSM152965 2 0.2469 0.782 0.000 0.892 0.000 0.108
#> GSM152966 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM152967 4 0.3528 0.713 0.000 0.192 0.000 0.808
#> GSM152968 2 0.4222 0.748 0.000 0.728 0.272 0.000
#> GSM152969 4 0.2647 0.759 0.000 0.120 0.000 0.880
#> GSM152970 4 0.0921 0.841 0.000 0.028 0.000 0.972
#> GSM152971 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM152972 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM152973 4 0.4424 0.715 0.000 0.100 0.088 0.812
#> GSM152974 2 0.2593 0.785 0.000 0.892 0.004 0.104
#> GSM152975 2 0.4967 0.190 0.000 0.548 0.000 0.452
#> GSM152976 4 0.0817 0.844 0.000 0.024 0.000 0.976
#> GSM152977 4 0.2081 0.808 0.000 0.084 0.000 0.916
#> GSM152978 4 0.4500 0.419 0.000 0.316 0.000 0.684
#> GSM152979 2 0.4193 0.749 0.000 0.732 0.268 0.000
#> GSM152980 2 0.2081 0.787 0.000 0.916 0.000 0.084
#> GSM152981 2 0.4936 0.716 0.000 0.652 0.340 0.008
#> GSM152982 4 0.1022 0.832 0.000 0.032 0.000 0.968
#> GSM152983 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM152984 4 0.4199 0.756 0.000 0.164 0.032 0.804
#> GSM152985 4 0.1211 0.815 0.040 0.000 0.000 0.960
#> GSM152986 4 0.0000 0.847 0.000 0.000 0.000 1.000
#> GSM152987 1 0.2489 0.842 0.912 0.000 0.020 0.068
#> GSM152988 4 0.1022 0.830 0.000 0.032 0.000 0.968
#> GSM152989 4 0.0188 0.845 0.004 0.000 0.000 0.996
#> GSM152990 2 0.4343 0.750 0.000 0.732 0.264 0.004
#> GSM152991 2 0.5532 0.776 0.000 0.704 0.228 0.068
#> GSM187524 1 0.2081 0.846 0.916 0.000 0.084 0.000
#> GSM187525 1 0.1209 0.928 0.964 0.000 0.032 0.004
#> GSM187526 1 0.0895 0.942 0.976 0.000 0.020 0.004
#> GSM187527 3 0.6399 0.773 0.276 0.000 0.620 0.104
#> GSM152856 3 0.4790 0.923 0.380 0.000 0.620 0.000
#> GSM152857 3 0.6870 0.619 0.172 0.012 0.636 0.180
#> GSM152858 1 0.0188 0.949 0.996 0.000 0.004 0.000
#> GSM152859 1 0.0592 0.946 0.984 0.000 0.016 0.000
#> GSM152860 1 0.0188 0.949 0.996 0.000 0.004 0.000
#> GSM152861 1 0.0336 0.951 0.992 0.000 0.008 0.000
#> GSM152862 1 0.0469 0.949 0.988 0.000 0.012 0.000
#> GSM152863 1 0.1610 0.916 0.952 0.000 0.032 0.016
#> GSM152864 1 0.0336 0.951 0.992 0.000 0.008 0.000
#> GSM152865 1 0.0336 0.951 0.992 0.000 0.008 0.000
#> GSM152866 3 0.4790 0.923 0.380 0.000 0.620 0.000
#> GSM152867 1 0.0336 0.951 0.992 0.000 0.008 0.000
#> GSM152868 1 0.0336 0.951 0.992 0.000 0.008 0.000
#> GSM152869 1 0.0336 0.951 0.992 0.000 0.008 0.000
#> GSM152870 1 0.0524 0.948 0.988 0.000 0.008 0.004
#> GSM152871 1 0.0188 0.949 0.996 0.000 0.004 0.000
#> GSM152872 1 0.0188 0.949 0.996 0.000 0.004 0.000
#> GSM152873 3 0.4790 0.923 0.380 0.000 0.620 0.000
#> GSM152874 3 0.4790 0.923 0.380 0.000 0.620 0.000
#> GSM152875 3 0.4790 0.923 0.380 0.000 0.620 0.000
#> GSM152876 3 0.5355 0.905 0.360 0.000 0.620 0.020
#> GSM152877 3 0.4790 0.923 0.380 0.000 0.620 0.000
#> GSM152878 3 0.5436 0.900 0.356 0.000 0.620 0.024
#> GSM152879 3 0.4790 0.923 0.380 0.000 0.620 0.000
#> GSM152880 3 0.4790 0.923 0.380 0.000 0.620 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.0404 0.7138 0.000 0.988 0.000 0.012 0.000
#> GSM152805 5 0.4883 0.8459 0.052 0.260 0.004 0.000 0.684
#> GSM152806 5 0.4883 0.8459 0.052 0.260 0.004 0.000 0.684
#> GSM152807 2 0.0609 0.7112 0.000 0.980 0.000 0.020 0.000
#> GSM152808 5 0.4883 0.8459 0.052 0.260 0.004 0.000 0.684
#> GSM152809 2 0.4045 0.1423 0.000 0.644 0.000 0.356 0.000
#> GSM152810 5 0.5493 0.4952 0.000 0.112 0.000 0.256 0.632
#> GSM152811 5 0.4842 0.8403 0.048 0.264 0.004 0.000 0.684
#> GSM152812 2 0.0404 0.7138 0.000 0.988 0.000 0.012 0.000
#> GSM152813 2 0.0404 0.7138 0.000 0.988 0.000 0.012 0.000
#> GSM152814 2 0.0404 0.7138 0.000 0.988 0.000 0.012 0.000
#> GSM152815 2 0.0510 0.7134 0.000 0.984 0.000 0.016 0.000
#> GSM152816 2 0.3884 0.5016 0.000 0.708 0.000 0.004 0.288
#> GSM152817 5 0.4883 0.8459 0.052 0.260 0.004 0.000 0.684
#> GSM152818 5 0.4883 0.8459 0.052 0.260 0.004 0.000 0.684
#> GSM152819 2 0.0324 0.7144 0.000 0.992 0.000 0.004 0.004
#> GSM152820 2 0.0963 0.7032 0.000 0.964 0.000 0.000 0.036
#> GSM152821 2 0.0510 0.7134 0.000 0.984 0.000 0.016 0.000
#> GSM153115 4 0.2424 0.7969 0.000 0.132 0.000 0.868 0.000
#> GSM153116 2 0.4130 0.4970 0.000 0.696 0.000 0.012 0.292
#> GSM153117 2 0.3756 0.5535 0.000 0.744 0.000 0.008 0.248
#> GSM153118 2 0.0000 0.7130 0.000 1.000 0.000 0.000 0.000
#> GSM153119 2 0.4403 0.3358 0.000 0.608 0.000 0.008 0.384
#> GSM153120 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM153121 2 0.5547 0.2091 0.000 0.564 0.000 0.080 0.356
#> GSM153122 2 0.4746 -0.1252 0.000 0.504 0.000 0.016 0.480
#> GSM153123 2 0.0703 0.7085 0.000 0.976 0.000 0.000 0.024
#> GSM153124 2 0.3210 0.5377 0.000 0.788 0.000 0.212 0.000
#> GSM153125 4 0.1341 0.8514 0.000 0.056 0.000 0.944 0.000
#> GSM153126 4 0.4401 0.4733 0.000 0.016 0.000 0.656 0.328
#> GSM153127 2 0.0510 0.7134 0.000 0.984 0.000 0.016 0.000
#> GSM153128 2 0.4249 0.5013 0.000 0.688 0.000 0.016 0.296
#> GSM153129 2 0.2763 0.6398 0.000 0.848 0.000 0.004 0.148
#> GSM153130 2 0.4225 0.3856 0.000 0.632 0.000 0.004 0.364
#> GSM153131 2 0.4166 0.4140 0.000 0.648 0.000 0.004 0.348
#> GSM153132 2 0.3895 0.4606 0.000 0.680 0.000 0.000 0.320
#> GSM153133 2 0.1502 0.6936 0.000 0.940 0.000 0.056 0.004
#> GSM153134 2 0.1704 0.6910 0.000 0.928 0.000 0.004 0.068
#> GSM153135 2 0.0609 0.7122 0.000 0.980 0.000 0.020 0.000
#> GSM153136 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM153137 2 0.0510 0.7134 0.000 0.984 0.000 0.016 0.000
#> GSM153138 2 0.0404 0.7138 0.000 0.988 0.000 0.012 0.000
#> GSM153139 2 0.4182 0.4084 0.000 0.644 0.000 0.004 0.352
#> GSM153140 2 0.0000 0.7130 0.000 1.000 0.000 0.000 0.000
#> GSM153141 2 0.0510 0.7134 0.000 0.984 0.000 0.016 0.000
#> GSM153142 5 0.4991 0.7455 0.040 0.320 0.004 0.000 0.636
#> GSM153143 2 0.3461 0.5223 0.000 0.772 0.000 0.224 0.004
#> GSM153144 2 0.3274 0.4316 0.000 0.780 0.000 0.220 0.000
#> GSM153145 5 0.4883 0.8459 0.052 0.260 0.004 0.000 0.684
#> GSM153146 2 0.0162 0.7139 0.000 0.996 0.000 0.004 0.000
#> GSM153147 4 0.6014 0.2894 0.000 0.172 0.000 0.576 0.252
#> GSM153148 2 0.0510 0.7134 0.000 0.984 0.000 0.016 0.000
#> GSM153149 2 0.0566 0.7151 0.000 0.984 0.000 0.012 0.004
#> GSM153150 4 0.1121 0.8597 0.000 0.044 0.000 0.956 0.000
#> GSM153151 2 0.4249 0.4812 0.000 0.688 0.000 0.016 0.296
#> GSM153152 2 0.4622 0.5068 0.000 0.684 0.000 0.040 0.276
#> GSM153153 2 0.0404 0.7138 0.000 0.988 0.000 0.012 0.000
#> GSM153154 2 0.4238 0.3837 0.000 0.628 0.000 0.004 0.368
#> GSM153155 2 0.0510 0.7134 0.000 0.984 0.000 0.016 0.000
#> GSM153156 2 0.4211 0.3937 0.000 0.636 0.000 0.004 0.360
#> GSM153157 2 0.4225 0.3856 0.000 0.632 0.000 0.004 0.364
#> GSM153158 2 0.3928 0.4905 0.000 0.700 0.000 0.004 0.296
#> GSM153159 2 0.4321 0.3062 0.000 0.600 0.000 0.004 0.396
#> GSM153160 5 0.6795 0.3847 0.000 0.288 0.000 0.348 0.364
#> GSM153161 2 0.0510 0.7134 0.000 0.984 0.000 0.016 0.000
#> GSM153162 4 0.5282 0.5160 0.000 0.088 0.000 0.644 0.268
#> GSM153163 2 0.4225 0.3856 0.000 0.632 0.000 0.004 0.364
#> GSM153164 2 0.1408 0.7045 0.000 0.948 0.000 0.008 0.044
#> GSM153165 2 0.4211 0.3937 0.000 0.636 0.000 0.004 0.360
#> GSM153166 2 0.0162 0.7118 0.000 0.996 0.000 0.004 0.000
#> GSM153167 2 0.0510 0.7109 0.000 0.984 0.000 0.000 0.016
#> GSM153168 5 0.4883 0.8459 0.052 0.260 0.004 0.000 0.684
#> GSM153169 2 0.4211 0.3937 0.000 0.636 0.000 0.004 0.360
#> GSM153170 2 0.4225 0.3856 0.000 0.632 0.000 0.004 0.364
#> GSM153171 4 0.2020 0.8224 0.000 0.100 0.000 0.900 0.000
#> GSM153172 2 0.0162 0.7139 0.000 0.996 0.000 0.004 0.000
#> GSM153173 2 0.4709 0.3440 0.000 0.612 0.000 0.024 0.364
#> GSM153174 4 0.3639 0.7330 0.000 0.184 0.000 0.792 0.024
#> GSM153175 4 0.0609 0.8689 0.000 0.020 0.000 0.980 0.000
#> GSM153176 4 0.1597 0.8423 0.000 0.012 0.000 0.940 0.048
#> GSM153177 2 0.1282 0.7054 0.000 0.952 0.000 0.004 0.044
#> GSM152931 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM152932 2 0.0693 0.7145 0.000 0.980 0.000 0.012 0.008
#> GSM152933 2 0.0000 0.7130 0.000 1.000 0.000 0.000 0.000
#> GSM152934 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM152935 2 0.3366 0.5880 0.000 0.784 0.000 0.004 0.212
#> GSM152936 4 0.2424 0.7976 0.000 0.132 0.000 0.868 0.000
#> GSM152937 2 0.4697 0.4206 0.000 0.648 0.000 0.032 0.320
#> GSM152938 2 0.5538 0.3538 0.000 0.644 0.000 0.144 0.212
#> GSM152939 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM152940 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM152941 1 0.3433 0.7261 0.832 0.004 0.032 0.132 0.000
#> GSM152942 4 0.3630 0.6797 0.000 0.016 0.000 0.780 0.204
#> GSM152943 2 0.3561 0.4755 0.000 0.740 0.000 0.260 0.000
#> GSM152944 2 0.4238 0.3774 0.000 0.628 0.000 0.004 0.368
#> GSM152945 2 0.2139 0.6917 0.000 0.916 0.000 0.032 0.052
#> GSM152946 2 0.0510 0.7137 0.000 0.984 0.000 0.016 0.000
#> GSM152947 4 0.0290 0.8695 0.000 0.008 0.000 0.992 0.000
#> GSM152948 2 0.0404 0.7138 0.000 0.988 0.000 0.012 0.000
#> GSM152949 4 0.6473 -0.2446 0.000 0.188 0.000 0.448 0.364
#> GSM152950 4 0.5915 0.1960 0.000 0.124 0.000 0.552 0.324
#> GSM152951 2 0.0794 0.7089 0.000 0.972 0.000 0.028 0.000
#> GSM152952 2 0.0510 0.7134 0.000 0.984 0.000 0.016 0.000
#> GSM152953 2 0.0404 0.7138 0.000 0.988 0.000 0.012 0.000
#> GSM152954 4 0.1121 0.8563 0.000 0.044 0.000 0.956 0.000
#> GSM152955 2 0.5074 0.4925 0.000 0.700 0.000 0.168 0.132
#> GSM152956 2 0.0510 0.7134 0.000 0.984 0.000 0.016 0.000
#> GSM152957 4 0.0404 0.8700 0.000 0.012 0.000 0.988 0.000
#> GSM152958 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM152959 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM152960 2 0.4297 0.0275 0.000 0.528 0.000 0.472 0.000
#> GSM152961 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM152962 2 0.4054 0.5555 0.000 0.748 0.000 0.028 0.224
#> GSM152963 2 0.0510 0.7134 0.000 0.984 0.000 0.016 0.000
#> GSM152964 2 0.5475 0.3044 0.000 0.596 0.000 0.084 0.320
#> GSM152965 2 0.0510 0.7134 0.000 0.984 0.000 0.016 0.000
#> GSM152966 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM152967 4 0.3661 0.6351 0.000 0.276 0.000 0.724 0.000
#> GSM152968 2 0.4225 0.3856 0.000 0.632 0.000 0.004 0.364
#> GSM152969 4 0.2377 0.7622 0.000 0.128 0.000 0.872 0.000
#> GSM152970 4 0.1121 0.8615 0.000 0.044 0.000 0.956 0.000
#> GSM152971 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM152972 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM152973 4 0.2771 0.7749 0.000 0.012 0.000 0.860 0.128
#> GSM152974 2 0.0451 0.7152 0.000 0.988 0.000 0.008 0.004
#> GSM152975 2 0.4126 0.1460 0.000 0.620 0.000 0.380 0.000
#> GSM152976 4 0.1043 0.8643 0.000 0.040 0.000 0.960 0.000
#> GSM152977 4 0.1043 0.8613 0.000 0.040 0.000 0.960 0.000
#> GSM152978 4 0.4015 0.3034 0.000 0.348 0.000 0.652 0.000
#> GSM152979 2 0.4211 0.3937 0.000 0.636 0.000 0.004 0.360
#> GSM152980 2 0.0000 0.7130 0.000 1.000 0.000 0.000 0.000
#> GSM152981 5 0.5045 0.2836 0.024 0.464 0.000 0.004 0.508
#> GSM152982 4 0.0451 0.8707 0.000 0.008 0.000 0.988 0.004
#> GSM152983 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM152984 4 0.3847 0.7354 0.000 0.180 0.000 0.784 0.036
#> GSM152985 4 0.0324 0.8688 0.004 0.004 0.000 0.992 0.000
#> GSM152986 4 0.0162 0.8708 0.000 0.004 0.000 0.996 0.000
#> GSM152987 1 0.3953 0.7834 0.792 0.000 0.148 0.060 0.000
#> GSM152988 4 0.0290 0.8695 0.000 0.008 0.000 0.992 0.000
#> GSM152989 4 0.0324 0.8688 0.004 0.004 0.000 0.992 0.000
#> GSM152990 2 0.4313 0.3950 0.000 0.636 0.000 0.008 0.356
#> GSM152991 2 0.4290 0.4904 0.000 0.680 0.000 0.016 0.304
#> GSM187524 1 0.3967 0.7087 0.724 0.000 0.264 0.000 0.012
#> GSM187525 1 0.3720 0.7619 0.760 0.000 0.228 0.000 0.012
#> GSM187526 1 0.2970 0.8080 0.828 0.000 0.168 0.004 0.000
#> GSM187527 3 0.0162 0.9950 0.004 0.000 0.996 0.000 0.000
#> GSM152856 3 0.0162 0.9950 0.004 0.000 0.996 0.000 0.000
#> GSM152857 3 0.0955 0.9447 0.000 0.000 0.968 0.028 0.004
#> GSM152858 1 0.4793 0.7760 0.684 0.000 0.056 0.000 0.260
#> GSM152859 1 0.5427 0.7543 0.636 0.000 0.104 0.000 0.260
#> GSM152860 1 0.4793 0.7765 0.684 0.000 0.056 0.000 0.260
#> GSM152861 1 0.2074 0.8337 0.896 0.000 0.104 0.000 0.000
#> GSM152862 1 0.5335 0.7634 0.644 0.000 0.096 0.000 0.260
#> GSM152863 1 0.2674 0.8286 0.868 0.000 0.120 0.012 0.000
#> GSM152864 1 0.2230 0.8333 0.884 0.000 0.116 0.000 0.000
#> GSM152865 1 0.2230 0.8333 0.884 0.000 0.116 0.000 0.000
#> GSM152866 3 0.0162 0.9950 0.004 0.000 0.996 0.000 0.000
#> GSM152867 1 0.2230 0.8333 0.884 0.000 0.116 0.000 0.000
#> GSM152868 1 0.2230 0.8333 0.884 0.000 0.116 0.000 0.000
#> GSM152869 1 0.2230 0.8333 0.884 0.000 0.116 0.000 0.000
#> GSM152870 1 0.5028 0.7736 0.668 0.000 0.072 0.000 0.260
#> GSM152871 1 0.4730 0.7766 0.688 0.000 0.052 0.000 0.260
#> GSM152872 1 0.4854 0.7759 0.680 0.000 0.060 0.000 0.260
#> GSM152873 3 0.0162 0.9950 0.004 0.000 0.996 0.000 0.000
#> GSM152874 3 0.0162 0.9950 0.004 0.000 0.996 0.000 0.000
#> GSM152875 3 0.0162 0.9950 0.004 0.000 0.996 0.000 0.000
#> GSM152876 3 0.0162 0.9950 0.004 0.000 0.996 0.000 0.000
#> GSM152877 3 0.0162 0.9950 0.004 0.000 0.996 0.000 0.000
#> GSM152878 3 0.0162 0.9950 0.004 0.000 0.996 0.000 0.000
#> GSM152879 3 0.0162 0.9950 0.004 0.000 0.996 0.000 0.000
#> GSM152880 3 0.0162 0.9950 0.004 0.000 0.996 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.0000 0.7923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152805 5 0.0363 0.8572 0.012 0.000 0.000 0.000 0.988 0.000
#> GSM152806 5 0.0000 0.8668 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152807 2 0.0858 0.7876 0.028 0.968 0.000 0.004 0.000 0.000
#> GSM152808 5 0.0000 0.8668 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152809 2 0.4181 0.3030 0.028 0.644 0.000 0.328 0.000 0.000
#> GSM152810 5 0.6141 0.4918 0.204 0.052 0.000 0.172 0.572 0.000
#> GSM152811 5 0.1007 0.8366 0.044 0.000 0.000 0.000 0.956 0.000
#> GSM152812 2 0.0260 0.7923 0.008 0.992 0.000 0.000 0.000 0.000
#> GSM152813 2 0.0000 0.7923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152814 2 0.0000 0.7923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152815 2 0.0713 0.7886 0.028 0.972 0.000 0.000 0.000 0.000
#> GSM152816 2 0.4595 0.7112 0.168 0.696 0.000 0.000 0.136 0.000
#> GSM152817 5 0.0000 0.8668 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152818 5 0.0000 0.8668 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152819 2 0.0547 0.7943 0.000 0.980 0.000 0.000 0.020 0.000
#> GSM152820 2 0.1168 0.7922 0.016 0.956 0.000 0.000 0.028 0.000
#> GSM152821 2 0.0260 0.7923 0.008 0.992 0.000 0.000 0.000 0.000
#> GSM153115 4 0.2135 0.7782 0.000 0.128 0.000 0.872 0.000 0.000
#> GSM153116 2 0.4767 0.7105 0.168 0.676 0.000 0.000 0.156 0.000
#> GSM153117 2 0.4104 0.7370 0.148 0.748 0.000 0.000 0.104 0.000
#> GSM153118 2 0.0146 0.7935 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM153119 2 0.5327 0.6538 0.208 0.596 0.000 0.000 0.196 0.000
#> GSM153120 4 0.0858 0.8393 0.028 0.004 0.000 0.968 0.000 0.000
#> GSM153121 2 0.6423 0.5982 0.212 0.548 0.000 0.076 0.164 0.000
#> GSM153122 2 0.6323 0.2797 0.200 0.416 0.000 0.020 0.364 0.000
#> GSM153123 2 0.0777 0.7939 0.024 0.972 0.000 0.000 0.004 0.000
#> GSM153124 2 0.2912 0.6806 0.000 0.784 0.000 0.216 0.000 0.000
#> GSM153125 4 0.1075 0.8327 0.000 0.048 0.000 0.952 0.000 0.000
#> GSM153126 4 0.4828 0.4996 0.200 0.000 0.000 0.664 0.136 0.000
#> GSM153127 2 0.0858 0.7893 0.028 0.968 0.000 0.000 0.004 0.000
#> GSM153128 2 0.4825 0.7069 0.180 0.668 0.000 0.000 0.152 0.000
#> GSM153129 2 0.3030 0.7708 0.056 0.848 0.000 0.004 0.092 0.000
#> GSM153130 2 0.5088 0.6674 0.200 0.632 0.000 0.000 0.168 0.000
#> GSM153131 2 0.5027 0.6741 0.200 0.640 0.000 0.000 0.160 0.000
#> GSM153132 2 0.4800 0.7002 0.164 0.672 0.000 0.000 0.164 0.000
#> GSM153133 2 0.1821 0.7824 0.024 0.928 0.000 0.040 0.008 0.000
#> GSM153134 2 0.1657 0.7900 0.056 0.928 0.000 0.000 0.016 0.000
#> GSM153135 2 0.0858 0.7883 0.028 0.968 0.000 0.004 0.000 0.000
#> GSM153136 4 0.0603 0.8430 0.016 0.004 0.000 0.980 0.000 0.000
#> GSM153137 2 0.0713 0.7886 0.028 0.972 0.000 0.000 0.000 0.000
#> GSM153138 2 0.0000 0.7923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM153139 2 0.5001 0.6770 0.196 0.644 0.000 0.000 0.160 0.000
#> GSM153140 2 0.0000 0.7923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM153141 2 0.0713 0.7886 0.028 0.972 0.000 0.000 0.000 0.000
#> GSM153142 5 0.4223 0.5182 0.076 0.204 0.000 0.000 0.720 0.000
#> GSM153143 2 0.3902 0.6735 0.028 0.748 0.000 0.212 0.012 0.000
#> GSM153144 2 0.3161 0.5933 0.008 0.776 0.000 0.216 0.000 0.000
#> GSM153145 5 0.0000 0.8668 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153146 2 0.0000 0.7923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM153147 4 0.6423 0.3725 0.192 0.156 0.000 0.560 0.092 0.000
#> GSM153148 2 0.0547 0.7906 0.020 0.980 0.000 0.000 0.000 0.000
#> GSM153149 2 0.0260 0.7941 0.008 0.992 0.000 0.000 0.000 0.000
#> GSM153150 4 0.1713 0.8267 0.028 0.044 0.000 0.928 0.000 0.000
#> GSM153151 2 0.4846 0.7001 0.188 0.676 0.000 0.004 0.132 0.000
#> GSM153152 2 0.5069 0.7152 0.208 0.672 0.000 0.024 0.096 0.000
#> GSM153153 2 0.0146 0.7924 0.004 0.996 0.000 0.000 0.000 0.000
#> GSM153154 2 0.5246 0.6664 0.212 0.608 0.000 0.000 0.180 0.000
#> GSM153155 2 0.0713 0.7886 0.028 0.972 0.000 0.000 0.000 0.000
#> GSM153156 2 0.5088 0.6674 0.200 0.632 0.000 0.000 0.168 0.000
#> GSM153157 2 0.5088 0.6674 0.200 0.632 0.000 0.000 0.168 0.000
#> GSM153158 2 0.4535 0.7135 0.144 0.704 0.000 0.000 0.152 0.000
#> GSM153159 2 0.5300 0.6400 0.188 0.600 0.000 0.000 0.212 0.000
#> GSM153160 4 0.7498 -0.0492 0.200 0.272 0.000 0.360 0.168 0.000
#> GSM153161 2 0.0713 0.7886 0.028 0.972 0.000 0.000 0.000 0.000
#> GSM153162 4 0.5564 0.5470 0.188 0.076 0.000 0.652 0.084 0.000
#> GSM153163 2 0.5088 0.6674 0.200 0.632 0.000 0.000 0.168 0.000
#> GSM153164 2 0.0865 0.7937 0.000 0.964 0.000 0.000 0.036 0.000
#> GSM153165 2 0.5088 0.6674 0.200 0.632 0.000 0.000 0.168 0.000
#> GSM153166 2 0.0291 0.7936 0.004 0.992 0.000 0.000 0.004 0.000
#> GSM153167 2 0.0603 0.7940 0.004 0.980 0.000 0.000 0.016 0.000
#> GSM153168 5 0.0000 0.8668 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153169 2 0.5062 0.6706 0.196 0.636 0.000 0.000 0.168 0.000
#> GSM153170 2 0.5088 0.6674 0.200 0.632 0.000 0.000 0.168 0.000
#> GSM153171 4 0.1910 0.7921 0.000 0.108 0.000 0.892 0.000 0.000
#> GSM153172 2 0.0000 0.7923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM153173 2 0.5657 0.6484 0.200 0.608 0.000 0.024 0.168 0.000
#> GSM153174 4 0.3441 0.7019 0.024 0.188 0.000 0.784 0.004 0.000
#> GSM153175 4 0.0260 0.8447 0.000 0.008 0.000 0.992 0.000 0.000
#> GSM153176 4 0.1349 0.8173 0.004 0.000 0.000 0.940 0.056 0.000
#> GSM153177 2 0.1196 0.7945 0.040 0.952 0.000 0.000 0.008 0.000
#> GSM152931 4 0.0000 0.8430 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152932 2 0.0405 0.7940 0.004 0.988 0.000 0.000 0.008 0.000
#> GSM152933 2 0.0405 0.7947 0.008 0.988 0.000 0.000 0.004 0.000
#> GSM152934 4 0.0858 0.8393 0.028 0.004 0.000 0.968 0.000 0.000
#> GSM152935 2 0.3715 0.7455 0.188 0.764 0.000 0.000 0.048 0.000
#> GSM152936 4 0.2653 0.7588 0.012 0.144 0.000 0.844 0.000 0.000
#> GSM152937 2 0.5592 0.6765 0.192 0.628 0.000 0.032 0.148 0.000
#> GSM152938 2 0.5794 0.6338 0.136 0.640 0.000 0.144 0.080 0.000
#> GSM152939 4 0.0000 0.8430 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152940 4 0.0146 0.8445 0.000 0.004 0.000 0.996 0.000 0.000
#> GSM152941 1 0.4640 0.7708 0.720 0.000 0.160 0.104 0.000 0.016
#> GSM152942 4 0.3663 0.6698 0.148 0.000 0.000 0.784 0.068 0.000
#> GSM152943 2 0.3770 0.6495 0.028 0.728 0.000 0.244 0.000 0.000
#> GSM152944 2 0.5091 0.6675 0.196 0.632 0.000 0.000 0.172 0.000
#> GSM152945 2 0.2188 0.7882 0.036 0.912 0.000 0.020 0.032 0.000
#> GSM152946 2 0.0458 0.7918 0.000 0.984 0.000 0.016 0.000 0.000
#> GSM152947 4 0.0000 0.8430 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152948 2 0.0000 0.7923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152949 4 0.7279 0.0896 0.216 0.188 0.000 0.432 0.164 0.000
#> GSM152950 4 0.6726 0.2922 0.216 0.124 0.000 0.520 0.140 0.000
#> GSM152951 2 0.1074 0.7874 0.028 0.960 0.000 0.012 0.000 0.000
#> GSM152952 2 0.0713 0.7886 0.028 0.972 0.000 0.000 0.000 0.000
#> GSM152953 2 0.0000 0.7923 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152954 4 0.0937 0.8347 0.000 0.040 0.000 0.960 0.000 0.000
#> GSM152955 2 0.5160 0.6847 0.052 0.692 0.000 0.164 0.092 0.000
#> GSM152956 2 0.0547 0.7908 0.020 0.980 0.000 0.000 0.000 0.000
#> GSM152957 4 0.0458 0.8441 0.000 0.016 0.000 0.984 0.000 0.000
#> GSM152958 4 0.0000 0.8430 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152959 4 0.0363 0.8436 0.012 0.000 0.000 0.988 0.000 0.000
#> GSM152960 2 0.4460 0.1762 0.028 0.520 0.000 0.452 0.000 0.000
#> GSM152961 4 0.0000 0.8430 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152962 2 0.4557 0.7351 0.180 0.724 0.000 0.020 0.076 0.000
#> GSM152963 2 0.0632 0.7897 0.024 0.976 0.000 0.000 0.000 0.000
#> GSM152964 2 0.6211 0.6376 0.208 0.576 0.000 0.072 0.144 0.000
#> GSM152965 2 0.0632 0.7898 0.024 0.976 0.000 0.000 0.000 0.000
#> GSM152966 4 0.0146 0.8445 0.000 0.004 0.000 0.996 0.000 0.000
#> GSM152967 4 0.3929 0.5990 0.028 0.272 0.000 0.700 0.000 0.000
#> GSM152968 2 0.5113 0.6669 0.204 0.628 0.000 0.000 0.168 0.000
#> GSM152969 4 0.2048 0.7522 0.000 0.120 0.000 0.880 0.000 0.000
#> GSM152970 4 0.1265 0.8363 0.008 0.044 0.000 0.948 0.000 0.000
#> GSM152971 4 0.0146 0.8445 0.000 0.004 0.000 0.996 0.000 0.000
#> GSM152972 4 0.0632 0.8412 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM152973 4 0.2826 0.7493 0.092 0.000 0.000 0.856 0.052 0.000
#> GSM152974 2 0.0790 0.7902 0.032 0.968 0.000 0.000 0.000 0.000
#> GSM152975 2 0.4264 0.3264 0.028 0.620 0.000 0.352 0.000 0.000
#> GSM152976 4 0.0865 0.8385 0.000 0.036 0.000 0.964 0.000 0.000
#> GSM152977 4 0.0547 0.8432 0.000 0.020 0.000 0.980 0.000 0.000
#> GSM152978 4 0.4238 0.3875 0.028 0.344 0.000 0.628 0.000 0.000
#> GSM152979 2 0.5088 0.6674 0.200 0.632 0.000 0.000 0.168 0.000
#> GSM152980 2 0.0146 0.7923 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM152981 2 0.5654 0.3279 0.152 0.444 0.000 0.000 0.404 0.000
#> GSM152982 4 0.0436 0.8447 0.004 0.004 0.000 0.988 0.004 0.000
#> GSM152983 4 0.0000 0.8430 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152984 4 0.3572 0.7150 0.024 0.168 0.000 0.792 0.016 0.000
#> GSM152985 4 0.0260 0.8439 0.008 0.000 0.000 0.992 0.000 0.000
#> GSM152986 4 0.0146 0.8445 0.000 0.004 0.000 0.996 0.000 0.000
#> GSM152987 1 0.4784 0.8321 0.736 0.000 0.096 0.056 0.000 0.112
#> GSM152988 4 0.0146 0.8441 0.000 0.004 0.000 0.996 0.000 0.000
#> GSM152989 4 0.0000 0.8430 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152990 2 0.5088 0.6674 0.200 0.632 0.000 0.000 0.168 0.000
#> GSM152991 2 0.4800 0.7082 0.164 0.672 0.000 0.000 0.164 0.000
#> GSM187524 1 0.5524 0.5575 0.560 0.000 0.236 0.000 0.000 0.204
#> GSM187525 1 0.3896 0.7760 0.744 0.000 0.052 0.000 0.000 0.204
#> GSM187526 1 0.3921 0.8646 0.768 0.000 0.116 0.000 0.000 0.116
#> GSM187527 6 0.0000 0.9993 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152856 6 0.0000 0.9993 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152857 6 0.0146 0.9925 0.000 0.000 0.000 0.004 0.000 0.996
#> GSM152858 3 0.0000 0.9666 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM152859 3 0.1204 0.9248 0.000 0.000 0.944 0.000 0.000 0.056
#> GSM152860 3 0.0146 0.9682 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM152861 1 0.3587 0.8935 0.772 0.000 0.188 0.000 0.000 0.040
#> GSM152862 3 0.1007 0.9411 0.000 0.000 0.956 0.000 0.000 0.044
#> GSM152863 1 0.3968 0.8942 0.756 0.000 0.180 0.004 0.000 0.060
#> GSM152864 1 0.3651 0.9000 0.772 0.000 0.180 0.000 0.000 0.048
#> GSM152865 1 0.3651 0.9000 0.772 0.000 0.180 0.000 0.000 0.048
#> GSM152866 6 0.0000 0.9993 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152867 1 0.3651 0.9000 0.772 0.000 0.180 0.000 0.000 0.048
#> GSM152868 1 0.3651 0.9000 0.772 0.000 0.180 0.000 0.000 0.048
#> GSM152869 1 0.3651 0.9000 0.772 0.000 0.180 0.000 0.000 0.048
#> GSM152870 3 0.0547 0.9639 0.000 0.000 0.980 0.000 0.000 0.020
#> GSM152871 3 0.0000 0.9666 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM152872 3 0.0146 0.9684 0.000 0.000 0.996 0.000 0.000 0.004
#> GSM152873 6 0.0000 0.9993 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152874 6 0.0000 0.9993 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152875 6 0.0000 0.9993 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152876 6 0.0000 0.9993 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152877 6 0.0000 0.9993 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152878 6 0.0000 0.9993 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152879 6 0.0000 0.9993 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152880 6 0.0000 0.9993 0.000 0.000 0.000 0.000 0.000 1.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> SD:pam 170 3.24e-26 2
#> SD:pam 161 2.90e-31 3
#> SD:pam 164 1.78e-29 4
#> SD:pam 130 2.82e-26 5
#> SD:pam 159 2.21e-32 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "mclust"]
# you can also extract it by
# res = res_list["SD:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.888 0.965 0.982 0.3173 0.701 0.701
#> 3 3 0.502 0.776 0.827 0.7478 0.729 0.616
#> 4 4 0.663 0.817 0.888 0.2053 0.874 0.718
#> 5 5 0.689 0.640 0.763 0.0968 0.862 0.602
#> 6 6 0.707 0.683 0.802 0.0770 0.886 0.577
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.979 0.000 1.000
#> GSM152805 2 0.7056 0.789 0.192 0.808
#> GSM152806 2 0.7056 0.789 0.192 0.808
#> GSM152807 2 0.0000 0.979 0.000 1.000
#> GSM152808 2 0.7056 0.789 0.192 0.808
#> GSM152809 2 0.0000 0.979 0.000 1.000
#> GSM152810 2 0.8386 0.673 0.268 0.732
#> GSM152811 2 0.7056 0.789 0.192 0.808
#> GSM152812 2 0.0000 0.979 0.000 1.000
#> GSM152813 2 0.0000 0.979 0.000 1.000
#> GSM152814 2 0.0000 0.979 0.000 1.000
#> GSM152815 2 0.0000 0.979 0.000 1.000
#> GSM152816 2 0.0000 0.979 0.000 1.000
#> GSM152817 2 0.7056 0.789 0.192 0.808
#> GSM152818 2 0.7056 0.789 0.192 0.808
#> GSM152819 2 0.0376 0.977 0.004 0.996
#> GSM152820 2 0.0000 0.979 0.000 1.000
#> GSM152821 2 0.0000 0.979 0.000 1.000
#> GSM153115 2 0.0000 0.979 0.000 1.000
#> GSM153116 2 0.0672 0.974 0.008 0.992
#> GSM153117 2 0.0376 0.977 0.004 0.996
#> GSM153118 2 0.0000 0.979 0.000 1.000
#> GSM153119 2 0.4022 0.913 0.080 0.920
#> GSM153120 2 0.0376 0.977 0.004 0.996
#> GSM153121 2 0.0000 0.979 0.000 1.000
#> GSM153122 2 0.4815 0.890 0.104 0.896
#> GSM153123 2 0.0000 0.979 0.000 1.000
#> GSM153124 2 0.0000 0.979 0.000 1.000
#> GSM153125 2 0.0000 0.979 0.000 1.000
#> GSM153126 2 0.0000 0.979 0.000 1.000
#> GSM153127 2 0.0000 0.979 0.000 1.000
#> GSM153128 2 0.0000 0.979 0.000 1.000
#> GSM153129 2 0.0000 0.979 0.000 1.000
#> GSM153130 2 0.0000 0.979 0.000 1.000
#> GSM153131 2 0.0000 0.979 0.000 1.000
#> GSM153132 2 0.0000 0.979 0.000 1.000
#> GSM153133 2 0.0000 0.979 0.000 1.000
#> GSM153134 2 0.0000 0.979 0.000 1.000
#> GSM153135 2 0.0000 0.979 0.000 1.000
#> GSM153136 2 0.0376 0.977 0.004 0.996
#> GSM153137 2 0.0000 0.979 0.000 1.000
#> GSM153138 2 0.0000 0.979 0.000 1.000
#> GSM153139 2 0.0000 0.979 0.000 1.000
#> GSM153140 2 0.0000 0.979 0.000 1.000
#> GSM153141 2 0.0000 0.979 0.000 1.000
#> GSM153142 2 0.4022 0.913 0.080 0.920
#> GSM153143 2 0.0000 0.979 0.000 1.000
#> GSM153144 2 0.0000 0.979 0.000 1.000
#> GSM153145 2 0.7056 0.789 0.192 0.808
#> GSM153146 2 0.0000 0.979 0.000 1.000
#> GSM153147 2 0.0000 0.979 0.000 1.000
#> GSM153148 2 0.0000 0.979 0.000 1.000
#> GSM153149 2 0.0000 0.979 0.000 1.000
#> GSM153150 2 0.0376 0.977 0.004 0.996
#> GSM153151 2 0.0000 0.979 0.000 1.000
#> GSM153152 2 0.0000 0.979 0.000 1.000
#> GSM153153 2 0.0000 0.979 0.000 1.000
#> GSM153154 2 0.0000 0.979 0.000 1.000
#> GSM153155 2 0.0000 0.979 0.000 1.000
#> GSM153156 2 0.0000 0.979 0.000 1.000
#> GSM153157 2 0.4022 0.913 0.080 0.920
#> GSM153158 2 0.0376 0.977 0.004 0.996
#> GSM153159 2 0.4022 0.913 0.080 0.920
#> GSM153160 2 0.0000 0.979 0.000 1.000
#> GSM153161 2 0.0000 0.979 0.000 1.000
#> GSM153162 2 0.0000 0.979 0.000 1.000
#> GSM153163 2 0.0000 0.979 0.000 1.000
#> GSM153164 2 0.0376 0.977 0.004 0.996
#> GSM153165 2 0.0000 0.979 0.000 1.000
#> GSM153166 2 0.0000 0.979 0.000 1.000
#> GSM153167 2 0.0000 0.979 0.000 1.000
#> GSM153168 2 0.7056 0.789 0.192 0.808
#> GSM153169 2 0.0000 0.979 0.000 1.000
#> GSM153170 2 0.0000 0.979 0.000 1.000
#> GSM153171 2 0.0376 0.977 0.004 0.996
#> GSM153172 2 0.0000 0.979 0.000 1.000
#> GSM153173 2 0.0000 0.979 0.000 1.000
#> GSM153174 2 0.0000 0.979 0.000 1.000
#> GSM153175 2 0.0000 0.979 0.000 1.000
#> GSM153176 2 0.0376 0.977 0.004 0.996
#> GSM153177 2 0.0000 0.979 0.000 1.000
#> GSM152931 2 0.0000 0.979 0.000 1.000
#> GSM152932 2 0.0000 0.979 0.000 1.000
#> GSM152933 2 0.0000 0.979 0.000 1.000
#> GSM152934 2 0.0000 0.979 0.000 1.000
#> GSM152935 2 0.0376 0.977 0.004 0.996
#> GSM152936 2 0.0000 0.979 0.000 1.000
#> GSM152937 2 0.0000 0.979 0.000 1.000
#> GSM152938 2 0.0000 0.979 0.000 1.000
#> GSM152939 2 0.0000 0.979 0.000 1.000
#> GSM152940 2 0.0376 0.977 0.004 0.996
#> GSM152941 1 0.3733 0.923 0.928 0.072
#> GSM152942 2 0.0000 0.979 0.000 1.000
#> GSM152943 2 0.0000 0.979 0.000 1.000
#> GSM152944 2 0.0000 0.979 0.000 1.000
#> GSM152945 2 0.0376 0.977 0.004 0.996
#> GSM152946 2 0.0000 0.979 0.000 1.000
#> GSM152947 2 0.0376 0.977 0.004 0.996
#> GSM152948 2 0.0000 0.979 0.000 1.000
#> GSM152949 2 0.0000 0.979 0.000 1.000
#> GSM152950 2 0.0000 0.979 0.000 1.000
#> GSM152951 2 0.0000 0.979 0.000 1.000
#> GSM152952 2 0.0000 0.979 0.000 1.000
#> GSM152953 2 0.0000 0.979 0.000 1.000
#> GSM152954 2 0.0376 0.977 0.004 0.996
#> GSM152955 2 0.0376 0.977 0.004 0.996
#> GSM152956 2 0.0000 0.979 0.000 1.000
#> GSM152957 2 0.0376 0.977 0.004 0.996
#> GSM152958 2 0.0376 0.977 0.004 0.996
#> GSM152959 2 0.0376 0.977 0.004 0.996
#> GSM152960 2 0.0000 0.979 0.000 1.000
#> GSM152961 2 0.0376 0.977 0.004 0.996
#> GSM152962 2 0.0000 0.979 0.000 1.000
#> GSM152963 2 0.0000 0.979 0.000 1.000
#> GSM152964 2 0.4022 0.913 0.080 0.920
#> GSM152965 2 0.0000 0.979 0.000 1.000
#> GSM152966 2 0.0000 0.979 0.000 1.000
#> GSM152967 2 0.0000 0.979 0.000 1.000
#> GSM152968 2 0.0000 0.979 0.000 1.000
#> GSM152969 2 0.0000 0.979 0.000 1.000
#> GSM152970 2 0.0938 0.971 0.012 0.988
#> GSM152971 2 0.0000 0.979 0.000 1.000
#> GSM152972 2 0.0000 0.979 0.000 1.000
#> GSM152973 2 0.0000 0.979 0.000 1.000
#> GSM152974 2 0.0000 0.979 0.000 1.000
#> GSM152975 2 0.0376 0.977 0.004 0.996
#> GSM152976 2 0.0376 0.977 0.004 0.996
#> GSM152977 2 0.3274 0.931 0.060 0.940
#> GSM152978 2 0.0376 0.977 0.004 0.996
#> GSM152979 2 0.0000 0.979 0.000 1.000
#> GSM152980 2 0.0000 0.979 0.000 1.000
#> GSM152981 2 0.7056 0.789 0.192 0.808
#> GSM152982 2 0.0000 0.979 0.000 1.000
#> GSM152983 2 0.0000 0.979 0.000 1.000
#> GSM152984 2 0.0000 0.979 0.000 1.000
#> GSM152985 2 0.8499 0.658 0.276 0.724
#> GSM152986 2 0.0376 0.977 0.004 0.996
#> GSM152987 1 0.1633 0.974 0.976 0.024
#> GSM152988 2 0.0000 0.979 0.000 1.000
#> GSM152989 2 0.0376 0.977 0.004 0.996
#> GSM152990 2 0.0000 0.979 0.000 1.000
#> GSM152991 2 0.0376 0.977 0.004 0.996
#> GSM187524 1 0.0000 0.996 1.000 0.000
#> GSM187525 1 0.0000 0.996 1.000 0.000
#> GSM187526 1 0.0000 0.996 1.000 0.000
#> GSM187527 1 0.0000 0.996 1.000 0.000
#> GSM152856 1 0.0000 0.996 1.000 0.000
#> GSM152857 1 0.0672 0.989 0.992 0.008
#> GSM152858 1 0.0000 0.996 1.000 0.000
#> GSM152859 1 0.0000 0.996 1.000 0.000
#> GSM152860 1 0.0000 0.996 1.000 0.000
#> GSM152861 1 0.0000 0.996 1.000 0.000
#> GSM152862 1 0.0000 0.996 1.000 0.000
#> GSM152863 1 0.0000 0.996 1.000 0.000
#> GSM152864 1 0.0000 0.996 1.000 0.000
#> GSM152865 1 0.0000 0.996 1.000 0.000
#> GSM152866 1 0.0000 0.996 1.000 0.000
#> GSM152867 1 0.0000 0.996 1.000 0.000
#> GSM152868 1 0.0000 0.996 1.000 0.000
#> GSM152869 1 0.0000 0.996 1.000 0.000
#> GSM152870 1 0.0000 0.996 1.000 0.000
#> GSM152871 1 0.0000 0.996 1.000 0.000
#> GSM152872 1 0.0000 0.996 1.000 0.000
#> GSM152873 1 0.0000 0.996 1.000 0.000
#> GSM152874 1 0.0000 0.996 1.000 0.000
#> GSM152875 1 0.0000 0.996 1.000 0.000
#> GSM152876 1 0.0000 0.996 1.000 0.000
#> GSM152877 1 0.0000 0.996 1.000 0.000
#> GSM152878 1 0.0000 0.996 1.000 0.000
#> GSM152879 1 0.0000 0.996 1.000 0.000
#> GSM152880 1 0.0000 0.996 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.6302 0.690 0.000 0.520 0.480
#> GSM152805 3 0.6111 0.581 0.000 0.396 0.604
#> GSM152806 3 0.6126 0.577 0.000 0.400 0.600
#> GSM152807 3 0.5363 0.270 0.000 0.276 0.724
#> GSM152808 3 0.6126 0.577 0.000 0.400 0.600
#> GSM152809 3 0.5529 0.188 0.000 0.296 0.704
#> GSM152810 3 0.8742 0.478 0.136 0.308 0.556
#> GSM152811 3 0.6126 0.577 0.000 0.400 0.600
#> GSM152812 3 0.3192 0.681 0.000 0.112 0.888
#> GSM152813 3 0.4974 0.411 0.000 0.236 0.764
#> GSM152814 3 0.1411 0.757 0.000 0.036 0.964
#> GSM152815 3 0.4346 0.551 0.000 0.184 0.816
#> GSM152816 3 0.4346 0.749 0.000 0.184 0.816
#> GSM152817 3 0.6126 0.577 0.000 0.400 0.600
#> GSM152818 3 0.6126 0.577 0.000 0.400 0.600
#> GSM152819 3 0.3752 0.760 0.000 0.144 0.856
#> GSM152820 3 0.2261 0.774 0.000 0.068 0.932
#> GSM152821 3 0.1289 0.759 0.000 0.032 0.968
#> GSM153115 2 0.5882 0.936 0.000 0.652 0.348
#> GSM153116 3 0.3816 0.758 0.000 0.148 0.852
#> GSM153117 3 0.3816 0.758 0.000 0.148 0.852
#> GSM153118 3 0.0892 0.767 0.000 0.020 0.980
#> GSM153119 3 0.6045 0.596 0.000 0.380 0.620
#> GSM153120 2 0.5882 0.936 0.000 0.652 0.348
#> GSM153121 3 0.3816 0.764 0.000 0.148 0.852
#> GSM153122 3 0.6095 0.585 0.000 0.392 0.608
#> GSM153123 3 0.1163 0.761 0.000 0.028 0.972
#> GSM153124 2 0.6192 0.818 0.000 0.580 0.420
#> GSM153125 2 0.5882 0.936 0.000 0.652 0.348
#> GSM153126 3 0.4605 0.739 0.000 0.204 0.796
#> GSM153127 3 0.2448 0.724 0.000 0.076 0.924
#> GSM153128 3 0.3482 0.762 0.000 0.128 0.872
#> GSM153129 3 0.0892 0.764 0.000 0.020 0.980
#> GSM153130 3 0.4605 0.739 0.000 0.204 0.796
#> GSM153131 3 0.3116 0.763 0.000 0.108 0.892
#> GSM153132 3 0.3482 0.765 0.000 0.128 0.872
#> GSM153133 3 0.1289 0.759 0.000 0.032 0.968
#> GSM153134 3 0.1964 0.776 0.000 0.056 0.944
#> GSM153135 3 0.4235 0.569 0.000 0.176 0.824
#> GSM153136 2 0.5882 0.936 0.000 0.652 0.348
#> GSM153137 3 0.5560 0.172 0.000 0.300 0.700
#> GSM153138 3 0.1289 0.759 0.000 0.032 0.968
#> GSM153139 3 0.3816 0.758 0.000 0.148 0.852
#> GSM153140 3 0.3192 0.682 0.000 0.112 0.888
#> GSM153141 3 0.3551 0.651 0.000 0.132 0.868
#> GSM153142 3 0.6062 0.592 0.000 0.384 0.616
#> GSM153143 3 0.3267 0.677 0.000 0.116 0.884
#> GSM153144 3 0.2066 0.746 0.000 0.060 0.940
#> GSM153145 3 0.6126 0.577 0.000 0.400 0.600
#> GSM153146 3 0.1289 0.759 0.000 0.032 0.968
#> GSM153147 3 0.1163 0.765 0.000 0.028 0.972
#> GSM153148 3 0.1753 0.748 0.000 0.048 0.952
#> GSM153149 3 0.1289 0.759 0.000 0.032 0.968
#> GSM153150 2 0.5882 0.936 0.000 0.652 0.348
#> GSM153151 3 0.1163 0.761 0.000 0.028 0.972
#> GSM153152 3 0.0892 0.773 0.000 0.020 0.980
#> GSM153153 3 0.1289 0.759 0.000 0.032 0.968
#> GSM153154 3 0.3752 0.760 0.000 0.144 0.856
#> GSM153155 3 0.1289 0.759 0.000 0.032 0.968
#> GSM153156 3 0.4062 0.758 0.000 0.164 0.836
#> GSM153157 3 0.6008 0.603 0.000 0.372 0.628
#> GSM153158 3 0.3816 0.758 0.000 0.148 0.852
#> GSM153159 3 0.5835 0.631 0.000 0.340 0.660
#> GSM153160 3 0.4605 0.739 0.000 0.204 0.796
#> GSM153161 3 0.3686 0.639 0.000 0.140 0.860
#> GSM153162 3 0.3116 0.771 0.000 0.108 0.892
#> GSM153163 3 0.4605 0.739 0.000 0.204 0.796
#> GSM153164 3 0.3752 0.760 0.000 0.144 0.856
#> GSM153165 3 0.3752 0.760 0.000 0.144 0.856
#> GSM153166 3 0.1031 0.763 0.000 0.024 0.976
#> GSM153167 3 0.1289 0.759 0.000 0.032 0.968
#> GSM153168 3 0.6126 0.577 0.000 0.400 0.600
#> GSM153169 3 0.4654 0.737 0.000 0.208 0.792
#> GSM153170 3 0.3551 0.764 0.000 0.132 0.868
#> GSM153171 2 0.5882 0.936 0.000 0.652 0.348
#> GSM153172 3 0.1289 0.759 0.000 0.032 0.968
#> GSM153173 3 0.3879 0.759 0.000 0.152 0.848
#> GSM153174 3 0.3192 0.681 0.000 0.112 0.888
#> GSM153175 2 0.5882 0.936 0.000 0.652 0.348
#> GSM153176 2 0.6008 0.909 0.000 0.628 0.372
#> GSM153177 3 0.0892 0.764 0.000 0.020 0.980
#> GSM152931 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152932 3 0.1289 0.759 0.000 0.032 0.968
#> GSM152933 3 0.1289 0.773 0.000 0.032 0.968
#> GSM152934 3 0.5529 0.252 0.000 0.296 0.704
#> GSM152935 3 0.2959 0.772 0.000 0.100 0.900
#> GSM152936 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152937 3 0.2448 0.745 0.000 0.076 0.924
#> GSM152938 3 0.2356 0.744 0.000 0.072 0.928
#> GSM152939 2 0.5905 0.932 0.000 0.648 0.352
#> GSM152940 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152941 2 0.6696 0.274 0.348 0.632 0.020
#> GSM152942 3 0.2537 0.749 0.000 0.080 0.920
#> GSM152943 3 0.4062 0.635 0.000 0.164 0.836
#> GSM152944 3 0.3816 0.758 0.000 0.148 0.852
#> GSM152945 3 0.1860 0.762 0.000 0.052 0.948
#> GSM152946 3 0.5650 0.114 0.000 0.312 0.688
#> GSM152947 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152948 3 0.5650 0.114 0.000 0.312 0.688
#> GSM152949 3 0.3267 0.769 0.000 0.116 0.884
#> GSM152950 3 0.0000 0.770 0.000 0.000 1.000
#> GSM152951 3 0.4235 0.568 0.000 0.176 0.824
#> GSM152952 3 0.4062 0.595 0.000 0.164 0.836
#> GSM152953 3 0.2537 0.720 0.000 0.080 0.920
#> GSM152954 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152955 3 0.3482 0.763 0.000 0.128 0.872
#> GSM152956 3 0.2959 0.697 0.000 0.100 0.900
#> GSM152957 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152958 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152959 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152960 2 0.6045 0.892 0.000 0.620 0.380
#> GSM152961 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152962 3 0.0747 0.773 0.000 0.016 0.984
#> GSM152963 3 0.1753 0.748 0.000 0.048 0.952
#> GSM152964 3 0.4605 0.727 0.000 0.204 0.796
#> GSM152965 3 0.1289 0.759 0.000 0.032 0.968
#> GSM152966 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152967 3 0.4062 0.593 0.000 0.164 0.836
#> GSM152968 3 0.3340 0.768 0.000 0.120 0.880
#> GSM152969 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152970 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152971 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152972 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152973 2 0.5905 0.932 0.000 0.648 0.352
#> GSM152974 3 0.1289 0.759 0.000 0.032 0.968
#> GSM152975 3 0.3941 0.621 0.000 0.156 0.844
#> GSM152976 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152977 2 0.6126 0.865 0.000 0.600 0.400
#> GSM152978 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152979 3 0.3686 0.761 0.000 0.140 0.860
#> GSM152980 3 0.3482 0.676 0.000 0.128 0.872
#> GSM152981 3 0.6126 0.577 0.000 0.400 0.600
#> GSM152982 2 0.5988 0.912 0.000 0.632 0.368
#> GSM152983 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152984 2 0.6192 0.830 0.000 0.580 0.420
#> GSM152985 2 0.7848 0.508 0.264 0.640 0.096
#> GSM152986 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152987 2 0.6470 0.249 0.356 0.632 0.012
#> GSM152988 2 0.5905 0.932 0.000 0.648 0.352
#> GSM152989 2 0.5882 0.936 0.000 0.652 0.348
#> GSM152990 3 0.3619 0.764 0.000 0.136 0.864
#> GSM152991 3 0.3686 0.761 0.000 0.140 0.860
#> GSM187524 1 0.0000 0.998 1.000 0.000 0.000
#> GSM187525 1 0.0000 0.998 1.000 0.000 0.000
#> GSM187526 1 0.0000 0.998 1.000 0.000 0.000
#> GSM187527 1 0.0237 0.994 0.996 0.004 0.000
#> GSM152856 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152857 1 0.1636 0.963 0.964 0.020 0.016
#> GSM152858 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152859 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152860 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152861 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152862 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152863 1 0.0237 0.994 0.996 0.004 0.000
#> GSM152864 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152866 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152867 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152870 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152871 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152873 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152874 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152875 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152876 1 0.0237 0.994 0.996 0.004 0.000
#> GSM152877 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152878 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152879 1 0.0000 0.998 1.000 0.000 0.000
#> GSM152880 1 0.0000 0.998 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.4713 0.6751 0.000 0.640 0.000 0.360
#> GSM152805 3 0.4998 0.0203 0.000 0.488 0.512 0.000
#> GSM152806 3 0.1022 0.8045 0.000 0.032 0.968 0.000
#> GSM152807 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM152808 3 0.1022 0.8045 0.000 0.032 0.968 0.000
#> GSM152809 2 0.3942 0.8262 0.000 0.764 0.000 0.236
#> GSM152810 3 0.1998 0.7685 0.016 0.020 0.944 0.020
#> GSM152811 3 0.1637 0.8101 0.000 0.060 0.940 0.000
#> GSM152812 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM152813 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM152814 2 0.3801 0.8328 0.000 0.780 0.000 0.220
#> GSM152815 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM152816 2 0.2944 0.6615 0.000 0.868 0.128 0.004
#> GSM152817 3 0.1022 0.8045 0.000 0.032 0.968 0.000
#> GSM152818 3 0.2704 0.7730 0.000 0.124 0.876 0.000
#> GSM152819 2 0.2142 0.8045 0.000 0.928 0.016 0.056
#> GSM152820 2 0.1637 0.8112 0.000 0.940 0.000 0.060
#> GSM152821 2 0.3801 0.8328 0.000 0.780 0.000 0.220
#> GSM153115 4 0.0188 0.9185 0.000 0.004 0.000 0.996
#> GSM153116 2 0.3791 0.5816 0.000 0.796 0.200 0.004
#> GSM153117 2 0.2125 0.7377 0.000 0.920 0.076 0.004
#> GSM153118 2 0.3764 0.8335 0.000 0.784 0.000 0.216
#> GSM153119 3 0.2081 0.8069 0.000 0.084 0.916 0.000
#> GSM153120 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM153121 2 0.0592 0.7776 0.000 0.984 0.016 0.000
#> GSM153122 3 0.1716 0.8102 0.000 0.064 0.936 0.000
#> GSM153123 2 0.3024 0.8314 0.000 0.852 0.000 0.148
#> GSM153124 4 0.3907 0.5804 0.000 0.232 0.000 0.768
#> GSM153125 4 0.0188 0.9185 0.000 0.004 0.000 0.996
#> GSM153126 2 0.2530 0.6857 0.000 0.888 0.112 0.000
#> GSM153127 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM153128 3 0.6503 0.3847 0.000 0.448 0.480 0.072
#> GSM153129 2 0.1022 0.8028 0.000 0.968 0.000 0.032
#> GSM153130 2 0.2530 0.6857 0.000 0.888 0.112 0.000
#> GSM153131 2 0.0937 0.7824 0.000 0.976 0.012 0.012
#> GSM153132 2 0.0000 0.7854 0.000 1.000 0.000 0.000
#> GSM153133 2 0.3837 0.8323 0.000 0.776 0.000 0.224
#> GSM153134 2 0.0188 0.7882 0.000 0.996 0.000 0.004
#> GSM153135 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM153136 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM153137 2 0.4164 0.8023 0.000 0.736 0.000 0.264
#> GSM153138 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM153139 2 0.0000 0.7854 0.000 1.000 0.000 0.000
#> GSM153140 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM153141 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM153142 3 0.1637 0.8112 0.000 0.060 0.940 0.000
#> GSM153143 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM153144 2 0.3764 0.8337 0.000 0.784 0.000 0.216
#> GSM153145 3 0.1022 0.8045 0.000 0.032 0.968 0.000
#> GSM153146 2 0.3801 0.8328 0.000 0.780 0.000 0.220
#> GSM153147 2 0.0921 0.8010 0.000 0.972 0.000 0.028
#> GSM153148 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM153149 2 0.3688 0.8339 0.000 0.792 0.000 0.208
#> GSM153150 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM153151 2 0.3764 0.8338 0.000 0.784 0.000 0.216
#> GSM153152 2 0.0336 0.7907 0.000 0.992 0.000 0.008
#> GSM153153 2 0.3764 0.8335 0.000 0.784 0.000 0.216
#> GSM153154 2 0.0000 0.7854 0.000 1.000 0.000 0.000
#> GSM153155 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM153156 2 0.0469 0.7798 0.000 0.988 0.012 0.000
#> GSM153157 3 0.2469 0.7993 0.000 0.108 0.892 0.000
#> GSM153158 2 0.2197 0.7334 0.000 0.916 0.080 0.004
#> GSM153159 3 0.4697 0.5797 0.000 0.356 0.644 0.000
#> GSM153160 2 0.2530 0.6857 0.000 0.888 0.112 0.000
#> GSM153161 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM153162 2 0.0000 0.7854 0.000 1.000 0.000 0.000
#> GSM153163 2 0.2408 0.6950 0.000 0.896 0.104 0.000
#> GSM153164 2 0.2563 0.8079 0.000 0.908 0.020 0.072
#> GSM153165 2 0.0592 0.7775 0.000 0.984 0.016 0.000
#> GSM153166 2 0.1867 0.8172 0.000 0.928 0.000 0.072
#> GSM153167 2 0.3486 0.8344 0.000 0.812 0.000 0.188
#> GSM153168 3 0.1022 0.8045 0.000 0.032 0.968 0.000
#> GSM153169 2 0.2469 0.6906 0.000 0.892 0.108 0.000
#> GSM153170 2 0.0000 0.7854 0.000 1.000 0.000 0.000
#> GSM153171 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM153172 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM153173 2 0.2281 0.7040 0.000 0.904 0.096 0.000
#> GSM153174 2 0.2589 0.8241 0.000 0.884 0.000 0.116
#> GSM153175 4 0.0657 0.9124 0.000 0.004 0.012 0.984
#> GSM153176 4 0.4361 0.6245 0.000 0.208 0.020 0.772
#> GSM153177 2 0.2647 0.8264 0.000 0.880 0.000 0.120
#> GSM152931 4 0.0188 0.9185 0.000 0.004 0.000 0.996
#> GSM152932 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM152933 2 0.3356 0.8333 0.000 0.824 0.000 0.176
#> GSM152934 4 0.4123 0.7029 0.000 0.136 0.044 0.820
#> GSM152935 2 0.2216 0.8178 0.000 0.908 0.000 0.092
#> GSM152936 4 0.0188 0.9185 0.000 0.004 0.000 0.996
#> GSM152937 3 0.5999 0.5530 0.000 0.404 0.552 0.044
#> GSM152938 2 0.1406 0.7835 0.000 0.960 0.016 0.024
#> GSM152939 4 0.0927 0.9068 0.000 0.008 0.016 0.976
#> GSM152940 4 0.0188 0.9178 0.000 0.000 0.004 0.996
#> GSM152941 4 0.5182 0.4989 0.288 0.000 0.028 0.684
#> GSM152942 2 0.2021 0.7427 0.000 0.932 0.056 0.012
#> GSM152943 2 0.7641 0.3310 0.000 0.440 0.216 0.344
#> GSM152944 2 0.0000 0.7854 0.000 1.000 0.000 0.000
#> GSM152945 3 0.7687 0.1684 0.000 0.312 0.448 0.240
#> GSM152946 2 0.4040 0.8155 0.000 0.752 0.000 0.248
#> GSM152947 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152948 2 0.3942 0.8262 0.000 0.764 0.000 0.236
#> GSM152949 2 0.0000 0.7854 0.000 1.000 0.000 0.000
#> GSM152950 2 0.0336 0.7907 0.000 0.992 0.000 0.008
#> GSM152951 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM152952 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM152953 2 0.3942 0.8262 0.000 0.764 0.000 0.236
#> GSM152954 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152955 2 0.6682 0.2187 0.000 0.576 0.312 0.112
#> GSM152956 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM152957 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152958 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152959 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152960 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152961 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152962 2 0.1118 0.8038 0.000 0.964 0.000 0.036
#> GSM152963 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM152964 3 0.5839 0.6942 0.000 0.200 0.696 0.104
#> GSM152965 2 0.3801 0.8328 0.000 0.780 0.000 0.220
#> GSM152966 4 0.0188 0.9185 0.000 0.004 0.000 0.996
#> GSM152967 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM152968 2 0.0000 0.7854 0.000 1.000 0.000 0.000
#> GSM152969 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152970 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152971 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152972 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152973 4 0.4253 0.6348 0.000 0.208 0.016 0.776
#> GSM152974 2 0.3873 0.8312 0.000 0.772 0.000 0.228
#> GSM152975 2 0.4008 0.8215 0.000 0.756 0.000 0.244
#> GSM152976 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152977 4 0.0657 0.9115 0.000 0.004 0.012 0.984
#> GSM152978 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152979 2 0.0707 0.7753 0.000 0.980 0.020 0.000
#> GSM152980 2 0.4134 0.8064 0.000 0.740 0.000 0.260
#> GSM152981 3 0.1389 0.8084 0.000 0.048 0.952 0.000
#> GSM152982 4 0.0188 0.9185 0.000 0.004 0.000 0.996
#> GSM152983 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152984 4 0.5435 0.3356 0.000 0.420 0.016 0.564
#> GSM152985 4 0.3591 0.7117 0.168 0.000 0.008 0.824
#> GSM152986 4 0.0000 0.9207 0.000 0.000 0.000 1.000
#> GSM152987 4 0.5254 0.4746 0.300 0.000 0.028 0.672
#> GSM152988 4 0.1706 0.8805 0.000 0.036 0.016 0.948
#> GSM152989 4 0.0188 0.9191 0.000 0.000 0.004 0.996
#> GSM152990 2 0.0188 0.7837 0.000 0.996 0.004 0.000
#> GSM152991 2 0.5279 0.4776 0.000 0.716 0.232 0.052
#> GSM187524 1 0.0921 0.9760 0.972 0.000 0.028 0.000
#> GSM187525 1 0.0921 0.9760 0.972 0.000 0.028 0.000
#> GSM187526 1 0.0817 0.9775 0.976 0.000 0.024 0.000
#> GSM187527 1 0.1722 0.9395 0.944 0.000 0.008 0.048
#> GSM152856 1 0.0188 0.9838 0.996 0.000 0.004 0.000
#> GSM152857 1 0.4185 0.8429 0.844 0.016 0.080 0.060
#> GSM152858 1 0.0188 0.9830 0.996 0.000 0.004 0.000
#> GSM152859 1 0.0921 0.9760 0.972 0.000 0.028 0.000
#> GSM152860 1 0.0921 0.9760 0.972 0.000 0.028 0.000
#> GSM152861 1 0.0188 0.9838 0.996 0.000 0.004 0.000
#> GSM152862 1 0.0921 0.9760 0.972 0.000 0.028 0.000
#> GSM152863 1 0.0657 0.9773 0.984 0.000 0.004 0.012
#> GSM152864 1 0.0188 0.9838 0.996 0.000 0.004 0.000
#> GSM152865 1 0.0188 0.9838 0.996 0.000 0.004 0.000
#> GSM152866 1 0.0188 0.9830 0.996 0.000 0.004 0.000
#> GSM152867 1 0.0188 0.9838 0.996 0.000 0.004 0.000
#> GSM152868 1 0.0188 0.9838 0.996 0.000 0.004 0.000
#> GSM152869 1 0.0188 0.9838 0.996 0.000 0.004 0.000
#> GSM152870 1 0.0921 0.9760 0.972 0.000 0.028 0.000
#> GSM152871 1 0.0188 0.9830 0.996 0.000 0.004 0.000
#> GSM152872 1 0.0188 0.9830 0.996 0.000 0.004 0.000
#> GSM152873 1 0.0188 0.9838 0.996 0.000 0.004 0.000
#> GSM152874 1 0.0188 0.9838 0.996 0.000 0.004 0.000
#> GSM152875 1 0.0188 0.9825 0.996 0.000 0.000 0.004
#> GSM152876 1 0.0921 0.9634 0.972 0.000 0.000 0.028
#> GSM152877 1 0.0188 0.9838 0.996 0.000 0.004 0.000
#> GSM152878 1 0.0188 0.9838 0.996 0.000 0.004 0.000
#> GSM152879 1 0.0188 0.9838 0.996 0.000 0.004 0.000
#> GSM152880 1 0.0188 0.9838 0.996 0.000 0.004 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 3 0.6000 -0.4528 0.000 0.428 0.460 0.112 0.000
#> GSM152805 5 0.2966 0.7046 0.000 0.000 0.184 0.000 0.816
#> GSM152806 5 0.0000 0.8537 0.000 0.000 0.000 0.000 1.000
#> GSM152807 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM152808 5 0.0000 0.8537 0.000 0.000 0.000 0.000 1.000
#> GSM152809 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM152810 5 0.1894 0.8717 0.000 0.008 0.072 0.000 0.920
#> GSM152811 5 0.1608 0.8724 0.000 0.000 0.072 0.000 0.928
#> GSM152812 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM152813 2 0.5476 0.8740 0.000 0.544 0.388 0.068 0.000
#> GSM152814 2 0.5095 0.8463 0.000 0.560 0.400 0.040 0.000
#> GSM152815 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM152816 3 0.2104 0.5753 0.000 0.024 0.916 0.000 0.060
#> GSM152817 5 0.0000 0.8537 0.000 0.000 0.000 0.000 1.000
#> GSM152818 5 0.0963 0.8532 0.000 0.000 0.036 0.000 0.964
#> GSM152819 3 0.2732 0.5402 0.000 0.160 0.840 0.000 0.000
#> GSM152820 3 0.2891 0.5035 0.000 0.176 0.824 0.000 0.000
#> GSM152821 2 0.5365 0.8261 0.000 0.528 0.416 0.056 0.000
#> GSM153115 4 0.0404 0.8917 0.000 0.012 0.000 0.988 0.000
#> GSM153116 3 0.3800 0.5644 0.000 0.108 0.812 0.000 0.080
#> GSM153117 3 0.3838 0.3178 0.000 0.280 0.716 0.000 0.004
#> GSM153118 3 0.5296 -0.6627 0.000 0.472 0.480 0.048 0.000
#> GSM153119 5 0.2966 0.8382 0.000 0.016 0.136 0.000 0.848
#> GSM153120 4 0.0162 0.8933 0.000 0.004 0.000 0.996 0.000
#> GSM153121 3 0.0162 0.6064 0.000 0.000 0.996 0.000 0.004
#> GSM153122 5 0.1608 0.8724 0.000 0.000 0.072 0.000 0.928
#> GSM153123 3 0.4663 -0.1661 0.000 0.376 0.604 0.020 0.000
#> GSM153124 4 0.6080 0.2859 0.000 0.200 0.228 0.572 0.000
#> GSM153125 4 0.0290 0.8927 0.000 0.008 0.000 0.992 0.000
#> GSM153126 3 0.2582 0.5585 0.000 0.024 0.892 0.004 0.080
#> GSM153127 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM153128 3 0.5789 0.1344 0.000 0.088 0.620 0.016 0.276
#> GSM153129 3 0.3661 0.2930 0.000 0.276 0.724 0.000 0.000
#> GSM153130 3 0.2351 0.5609 0.000 0.016 0.896 0.000 0.088
#> GSM153131 3 0.1124 0.6026 0.000 0.036 0.960 0.004 0.000
#> GSM153132 3 0.3274 0.4299 0.000 0.220 0.780 0.000 0.000
#> GSM153133 3 0.5431 -0.5193 0.000 0.424 0.516 0.060 0.000
#> GSM153134 3 0.3707 0.2665 0.000 0.284 0.716 0.000 0.000
#> GSM153135 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM153136 4 0.0000 0.8936 0.000 0.000 0.000 1.000 0.000
#> GSM153137 2 0.6000 0.8177 0.000 0.532 0.340 0.128 0.000
#> GSM153138 2 0.5500 0.8824 0.000 0.552 0.376 0.072 0.000
#> GSM153139 3 0.0162 0.6063 0.000 0.000 0.996 0.000 0.004
#> GSM153140 2 0.5449 0.8839 0.000 0.556 0.376 0.068 0.000
#> GSM153141 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM153142 5 0.4525 0.6194 0.000 0.016 0.360 0.000 0.624
#> GSM153143 2 0.5418 0.8904 0.000 0.568 0.364 0.068 0.000
#> GSM153144 3 0.5095 -0.3719 0.000 0.400 0.560 0.040 0.000
#> GSM153145 5 0.0000 0.8537 0.000 0.000 0.000 0.000 1.000
#> GSM153146 2 0.5386 0.8619 0.000 0.544 0.396 0.060 0.000
#> GSM153147 3 0.2891 0.4916 0.000 0.176 0.824 0.000 0.000
#> GSM153148 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM153149 3 0.5009 -0.4313 0.000 0.428 0.540 0.032 0.000
#> GSM153150 4 0.0404 0.8927 0.000 0.012 0.000 0.988 0.000
#> GSM153151 3 0.5401 -0.4469 0.000 0.404 0.536 0.060 0.000
#> GSM153152 3 0.3707 0.2720 0.000 0.284 0.716 0.000 0.000
#> GSM153153 2 0.5234 0.7138 0.000 0.496 0.460 0.044 0.000
#> GSM153154 3 0.1197 0.5973 0.000 0.048 0.952 0.000 0.000
#> GSM153155 2 0.5447 0.8549 0.000 0.536 0.400 0.064 0.000
#> GSM153156 3 0.0290 0.6065 0.000 0.000 0.992 0.000 0.008
#> GSM153157 5 0.3055 0.8311 0.000 0.016 0.144 0.000 0.840
#> GSM153158 3 0.2735 0.5821 0.000 0.084 0.880 0.000 0.036
#> GSM153159 3 0.4702 -0.2668 0.000 0.016 0.552 0.000 0.432
#> GSM153160 3 0.2367 0.5674 0.000 0.020 0.904 0.004 0.072
#> GSM153161 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM153162 3 0.1851 0.5771 0.000 0.088 0.912 0.000 0.000
#> GSM153163 3 0.1914 0.5793 0.000 0.016 0.924 0.000 0.060
#> GSM153164 3 0.3932 0.1599 0.000 0.328 0.672 0.000 0.000
#> GSM153165 3 0.0404 0.6057 0.000 0.000 0.988 0.000 0.012
#> GSM153166 3 0.3949 0.1289 0.000 0.332 0.668 0.000 0.000
#> GSM153167 3 0.4537 -0.2042 0.000 0.396 0.592 0.012 0.000
#> GSM153168 5 0.0000 0.8537 0.000 0.000 0.000 0.000 1.000
#> GSM153169 3 0.2172 0.5692 0.000 0.016 0.908 0.000 0.076
#> GSM153170 3 0.0609 0.6036 0.000 0.020 0.980 0.000 0.000
#> GSM153171 4 0.0000 0.8936 0.000 0.000 0.000 1.000 0.000
#> GSM153172 2 0.5432 0.8662 0.000 0.544 0.392 0.064 0.000
#> GSM153173 3 0.1341 0.5881 0.000 0.000 0.944 0.000 0.056
#> GSM153174 3 0.4268 0.0099 0.000 0.344 0.648 0.008 0.000
#> GSM153175 4 0.1661 0.8644 0.000 0.024 0.036 0.940 0.000
#> GSM153176 4 0.3922 0.7122 0.000 0.040 0.180 0.780 0.000
#> GSM153177 3 0.4101 -0.0384 0.000 0.372 0.628 0.000 0.000
#> GSM152931 4 0.0609 0.8887 0.000 0.020 0.000 0.980 0.000
#> GSM152932 2 0.5341 0.7582 0.000 0.504 0.444 0.052 0.000
#> GSM152933 3 0.4658 -0.2790 0.000 0.408 0.576 0.016 0.000
#> GSM152934 4 0.5578 0.4952 0.000 0.180 0.176 0.644 0.000
#> GSM152935 3 0.4525 -0.0622 0.000 0.360 0.624 0.016 0.000
#> GSM152936 4 0.0162 0.8935 0.000 0.004 0.000 0.996 0.000
#> GSM152937 3 0.5877 -0.0533 0.000 0.052 0.596 0.036 0.316
#> GSM152938 3 0.0865 0.6003 0.000 0.024 0.972 0.004 0.000
#> GSM152939 4 0.2450 0.8232 0.000 0.028 0.076 0.896 0.000
#> GSM152940 4 0.0162 0.8933 0.000 0.004 0.000 0.996 0.000
#> GSM152941 4 0.6721 0.0581 0.304 0.276 0.000 0.420 0.000
#> GSM152942 3 0.1471 0.5938 0.000 0.024 0.952 0.004 0.020
#> GSM152943 2 0.7107 0.5105 0.000 0.500 0.224 0.240 0.036
#> GSM152944 3 0.0290 0.6064 0.000 0.000 0.992 0.000 0.008
#> GSM152945 2 0.7453 0.3326 0.000 0.452 0.328 0.076 0.144
#> GSM152946 3 0.5546 -0.5992 0.000 0.436 0.496 0.068 0.000
#> GSM152947 4 0.0963 0.8855 0.000 0.036 0.000 0.964 0.000
#> GSM152948 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM152949 3 0.0162 0.6058 0.000 0.004 0.996 0.000 0.000
#> GSM152950 3 0.2179 0.5650 0.000 0.112 0.888 0.000 0.000
#> GSM152951 2 0.5370 0.8953 0.000 0.584 0.348 0.068 0.000
#> GSM152952 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM152953 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM152954 4 0.0162 0.8933 0.000 0.004 0.000 0.996 0.000
#> GSM152955 3 0.6204 0.3380 0.000 0.212 0.640 0.064 0.084
#> GSM152956 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM152957 4 0.0794 0.8875 0.000 0.028 0.000 0.972 0.000
#> GSM152958 4 0.0162 0.8933 0.000 0.004 0.000 0.996 0.000
#> GSM152959 4 0.1410 0.8774 0.000 0.060 0.000 0.940 0.000
#> GSM152960 4 0.1364 0.8792 0.000 0.036 0.012 0.952 0.000
#> GSM152961 4 0.0703 0.8903 0.000 0.024 0.000 0.976 0.000
#> GSM152962 3 0.3163 0.5034 0.000 0.164 0.824 0.012 0.000
#> GSM152963 2 0.5357 0.8959 0.000 0.588 0.344 0.068 0.000
#> GSM152964 5 0.6213 0.5100 0.000 0.100 0.324 0.020 0.556
#> GSM152965 2 0.5408 0.8426 0.000 0.532 0.408 0.060 0.000
#> GSM152966 4 0.0290 0.8927 0.000 0.008 0.000 0.992 0.000
#> GSM152967 2 0.5467 0.8779 0.000 0.548 0.384 0.068 0.000
#> GSM152968 3 0.2230 0.5588 0.000 0.116 0.884 0.000 0.000
#> GSM152969 4 0.0162 0.8935 0.000 0.004 0.000 0.996 0.000
#> GSM152970 4 0.0880 0.8861 0.000 0.032 0.000 0.968 0.000
#> GSM152971 4 0.0162 0.8935 0.000 0.004 0.000 0.996 0.000
#> GSM152972 4 0.0162 0.8935 0.000 0.004 0.000 0.996 0.000
#> GSM152973 4 0.4666 0.6085 0.000 0.056 0.240 0.704 0.000
#> GSM152974 3 0.5267 -0.4899 0.000 0.428 0.524 0.048 0.000
#> GSM152975 2 0.5694 0.6211 0.000 0.460 0.460 0.080 0.000
#> GSM152976 4 0.1168 0.8860 0.000 0.032 0.008 0.960 0.000
#> GSM152977 4 0.2595 0.8286 0.000 0.032 0.080 0.888 0.000
#> GSM152978 4 0.0162 0.8936 0.000 0.000 0.004 0.996 0.000
#> GSM152979 3 0.0290 0.6065 0.000 0.000 0.992 0.000 0.008
#> GSM152980 2 0.5727 0.8331 0.000 0.560 0.340 0.100 0.000
#> GSM152981 5 0.1608 0.8724 0.000 0.000 0.072 0.000 0.928
#> GSM152982 4 0.1800 0.8623 0.000 0.048 0.020 0.932 0.000
#> GSM152983 4 0.0162 0.8935 0.000 0.004 0.000 0.996 0.000
#> GSM152984 3 0.5668 0.0161 0.000 0.080 0.504 0.416 0.000
#> GSM152985 4 0.2969 0.8132 0.020 0.128 0.000 0.852 0.000
#> GSM152986 4 0.0162 0.8933 0.000 0.004 0.000 0.996 0.000
#> GSM152987 4 0.6793 -0.0842 0.332 0.292 0.000 0.376 0.000
#> GSM152988 4 0.4210 0.7188 0.000 0.096 0.124 0.780 0.000
#> GSM152989 4 0.1792 0.8648 0.000 0.084 0.000 0.916 0.000
#> GSM152990 3 0.0000 0.6059 0.000 0.000 1.000 0.000 0.000
#> GSM152991 3 0.4254 0.5361 0.000 0.148 0.772 0.000 0.080
#> GSM187524 1 0.3816 0.7993 0.696 0.304 0.000 0.000 0.000
#> GSM187525 1 0.3816 0.7993 0.696 0.304 0.000 0.000 0.000
#> GSM187526 1 0.3796 0.8017 0.700 0.300 0.000 0.000 0.000
#> GSM187527 1 0.1195 0.8971 0.960 0.028 0.000 0.012 0.000
#> GSM152856 1 0.0162 0.9053 0.996 0.004 0.000 0.000 0.000
#> GSM152857 1 0.5790 0.5893 0.696 0.048 0.072 0.176 0.008
#> GSM152858 1 0.2732 0.8659 0.840 0.160 0.000 0.000 0.000
#> GSM152859 1 0.3707 0.8110 0.716 0.284 0.000 0.000 0.000
#> GSM152860 1 0.3796 0.8017 0.700 0.300 0.000 0.000 0.000
#> GSM152861 1 0.0404 0.9055 0.988 0.012 0.000 0.000 0.000
#> GSM152862 1 0.3774 0.8040 0.704 0.296 0.000 0.000 0.000
#> GSM152863 1 0.0609 0.9043 0.980 0.020 0.000 0.000 0.000
#> GSM152864 1 0.0162 0.9053 0.996 0.004 0.000 0.000 0.000
#> GSM152865 1 0.0404 0.9055 0.988 0.012 0.000 0.000 0.000
#> GSM152866 1 0.2852 0.8615 0.828 0.172 0.000 0.000 0.000
#> GSM152867 1 0.0162 0.9053 0.996 0.004 0.000 0.000 0.000
#> GSM152868 1 0.0162 0.9053 0.996 0.004 0.000 0.000 0.000
#> GSM152869 1 0.0162 0.9053 0.996 0.004 0.000 0.000 0.000
#> GSM152870 1 0.3796 0.8017 0.700 0.300 0.000 0.000 0.000
#> GSM152871 1 0.0794 0.9036 0.972 0.028 0.000 0.000 0.000
#> GSM152872 1 0.2852 0.8613 0.828 0.172 0.000 0.000 0.000
#> GSM152873 1 0.0162 0.9053 0.996 0.004 0.000 0.000 0.000
#> GSM152874 1 0.0162 0.9053 0.996 0.004 0.000 0.000 0.000
#> GSM152875 1 0.0404 0.9051 0.988 0.012 0.000 0.000 0.000
#> GSM152876 1 0.0609 0.9043 0.980 0.020 0.000 0.000 0.000
#> GSM152877 1 0.0162 0.9053 0.996 0.004 0.000 0.000 0.000
#> GSM152878 1 0.0162 0.9053 0.996 0.004 0.000 0.000 0.000
#> GSM152879 1 0.0162 0.9053 0.996 0.004 0.000 0.000 0.000
#> GSM152880 1 0.0290 0.9055 0.992 0.008 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.4077 0.55125 0.000 0.724 0.044 0.228 0.000 0.004
#> GSM152805 5 0.2003 0.82016 0.000 0.000 0.116 0.000 0.884 0.000
#> GSM152806 5 0.0146 0.85660 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM152807 2 0.3558 0.67544 0.000 0.760 0.000 0.028 0.000 0.212
#> GSM152808 5 0.0146 0.85660 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM152809 2 0.3727 0.67081 0.000 0.748 0.000 0.036 0.000 0.216
#> GSM152810 5 0.2800 0.81048 0.068 0.000 0.024 0.020 0.880 0.008
#> GSM152811 5 0.0713 0.85840 0.000 0.000 0.028 0.000 0.972 0.000
#> GSM152812 2 0.3641 0.67109 0.000 0.748 0.000 0.028 0.000 0.224
#> GSM152813 2 0.0870 0.71087 0.000 0.972 0.004 0.012 0.000 0.012
#> GSM152814 2 0.0984 0.71009 0.000 0.968 0.012 0.008 0.000 0.012
#> GSM152815 2 0.3641 0.67109 0.000 0.748 0.000 0.028 0.000 0.224
#> GSM152816 3 0.1924 0.74187 0.000 0.048 0.920 0.000 0.004 0.028
#> GSM152817 5 0.0146 0.85660 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM152818 5 0.0146 0.85660 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM152819 3 0.5567 0.61925 0.000 0.272 0.560 0.000 0.004 0.164
#> GSM152820 3 0.4561 0.41662 0.000 0.428 0.536 0.000 0.000 0.036
#> GSM152821 2 0.2955 0.63473 0.000 0.816 0.172 0.004 0.000 0.008
#> GSM153115 4 0.0508 0.94489 0.000 0.012 0.004 0.984 0.000 0.000
#> GSM153116 3 0.5737 0.63380 0.000 0.248 0.572 0.000 0.016 0.164
#> GSM153117 3 0.5870 0.59608 0.000 0.280 0.540 0.000 0.016 0.164
#> GSM153118 2 0.3121 0.61137 0.000 0.796 0.192 0.004 0.000 0.008
#> GSM153119 5 0.3375 0.81268 0.000 0.000 0.088 0.000 0.816 0.096
#> GSM153120 4 0.0547 0.93703 0.000 0.020 0.000 0.980 0.000 0.000
#> GSM153121 3 0.1524 0.75085 0.000 0.060 0.932 0.000 0.000 0.008
#> GSM153122 5 0.1444 0.84807 0.000 0.000 0.072 0.000 0.928 0.000
#> GSM153123 2 0.3652 0.50347 0.000 0.720 0.264 0.000 0.000 0.016
#> GSM153124 4 0.2709 0.80821 0.000 0.132 0.020 0.848 0.000 0.000
#> GSM153125 4 0.0603 0.94384 0.000 0.016 0.004 0.980 0.000 0.000
#> GSM153126 3 0.0806 0.70396 0.000 0.000 0.972 0.000 0.008 0.020
#> GSM153127 2 0.3668 0.66930 0.000 0.744 0.000 0.028 0.000 0.228
#> GSM153128 3 0.5596 0.67927 0.000 0.224 0.652 0.036 0.060 0.028
#> GSM153129 2 0.4434 0.00858 0.000 0.544 0.428 0.000 0.000 0.028
#> GSM153130 3 0.2039 0.60555 0.000 0.000 0.904 0.000 0.076 0.020
#> GSM153131 3 0.2500 0.75927 0.000 0.116 0.868 0.004 0.000 0.012
#> GSM153132 3 0.4249 0.61539 0.000 0.328 0.640 0.000 0.000 0.032
#> GSM153133 2 0.2806 0.65976 0.000 0.844 0.136 0.004 0.000 0.016
#> GSM153134 2 0.4429 0.07885 0.000 0.548 0.424 0.000 0.000 0.028
#> GSM153135 2 0.3668 0.66930 0.000 0.744 0.000 0.028 0.000 0.228
#> GSM153136 4 0.0363 0.94505 0.000 0.012 0.000 0.988 0.000 0.000
#> GSM153137 2 0.4174 0.61926 0.000 0.732 0.000 0.184 0.000 0.084
#> GSM153138 2 0.3692 0.66539 0.000 0.792 0.152 0.044 0.000 0.012
#> GSM153139 3 0.0717 0.72783 0.000 0.016 0.976 0.000 0.000 0.008
#> GSM153140 2 0.0870 0.71087 0.000 0.972 0.004 0.012 0.000 0.012
#> GSM153141 2 0.3668 0.66930 0.000 0.744 0.000 0.028 0.000 0.228
#> GSM153142 5 0.4918 0.58386 0.000 0.000 0.308 0.000 0.604 0.088
#> GSM153143 2 0.2173 0.70511 0.000 0.904 0.004 0.028 0.000 0.064
#> GSM153144 2 0.2555 0.67497 0.000 0.876 0.096 0.008 0.000 0.020
#> GSM153145 5 0.0146 0.85660 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM153146 2 0.2595 0.64854 0.000 0.836 0.160 0.004 0.000 0.000
#> GSM153147 3 0.4334 0.42763 0.000 0.408 0.568 0.000 0.000 0.024
#> GSM153148 2 0.3641 0.67062 0.000 0.748 0.000 0.028 0.000 0.224
#> GSM153149 2 0.3516 0.56996 0.000 0.760 0.220 0.004 0.000 0.016
#> GSM153150 4 0.0000 0.94385 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153151 2 0.4515 0.22910 0.000 0.608 0.356 0.008 0.000 0.028
#> GSM153152 2 0.4429 0.02901 0.000 0.548 0.424 0.000 0.000 0.028
#> GSM153153 2 0.2845 0.63574 0.000 0.820 0.172 0.004 0.000 0.004
#> GSM153154 3 0.3911 0.68417 0.000 0.256 0.712 0.000 0.000 0.032
#> GSM153155 2 0.2355 0.67544 0.000 0.876 0.112 0.004 0.000 0.008
#> GSM153156 3 0.1686 0.75027 0.000 0.064 0.924 0.000 0.000 0.012
#> GSM153157 5 0.3225 0.82018 0.000 0.000 0.080 0.000 0.828 0.092
#> GSM153158 3 0.5737 0.63380 0.000 0.248 0.572 0.000 0.016 0.164
#> GSM153159 5 0.5146 0.41389 0.000 0.000 0.396 0.000 0.516 0.088
#> GSM153160 3 0.0692 0.70549 0.000 0.000 0.976 0.000 0.004 0.020
#> GSM153161 2 0.3668 0.66930 0.000 0.744 0.000 0.028 0.000 0.228
#> GSM153162 3 0.3917 0.62401 0.000 0.284 0.692 0.000 0.000 0.024
#> GSM153163 3 0.0692 0.70549 0.000 0.000 0.976 0.000 0.004 0.020
#> GSM153164 3 0.5693 0.38121 0.000 0.392 0.448 0.000 0.000 0.160
#> GSM153165 3 0.1003 0.72113 0.000 0.016 0.964 0.000 0.000 0.020
#> GSM153166 2 0.3817 0.49941 0.000 0.720 0.252 0.000 0.000 0.028
#> GSM153167 2 0.3668 0.54756 0.000 0.744 0.228 0.000 0.000 0.028
#> GSM153168 5 0.0146 0.85660 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM153169 3 0.0806 0.70151 0.000 0.000 0.972 0.000 0.008 0.020
#> GSM153170 3 0.3098 0.74286 0.000 0.164 0.812 0.000 0.000 0.024
#> GSM153171 4 0.0260 0.94524 0.000 0.008 0.000 0.992 0.000 0.000
#> GSM153172 2 0.0984 0.71009 0.000 0.968 0.012 0.008 0.000 0.012
#> GSM153173 3 0.1053 0.71393 0.000 0.012 0.964 0.000 0.004 0.020
#> GSM153174 2 0.4227 0.33213 0.000 0.632 0.344 0.004 0.000 0.020
#> GSM153175 4 0.0870 0.94202 0.000 0.012 0.012 0.972 0.000 0.004
#> GSM153176 4 0.2976 0.81192 0.000 0.016 0.128 0.844 0.004 0.008
#> GSM153177 2 0.3534 0.52403 0.000 0.740 0.244 0.000 0.000 0.016
#> GSM152931 4 0.0725 0.94281 0.000 0.012 0.012 0.976 0.000 0.000
#> GSM152932 2 0.2531 0.66863 0.000 0.860 0.128 0.004 0.000 0.008
#> GSM152933 2 0.3509 0.52988 0.000 0.744 0.240 0.000 0.000 0.016
#> GSM152934 4 0.4455 0.56279 0.000 0.232 0.080 0.688 0.000 0.000
#> GSM152935 3 0.5383 0.39724 0.000 0.416 0.472 0.000 0.000 0.112
#> GSM152936 4 0.0291 0.94498 0.000 0.004 0.004 0.992 0.000 0.000
#> GSM152937 3 0.4418 0.71702 0.000 0.100 0.772 0.044 0.080 0.004
#> GSM152938 3 0.2454 0.75833 0.000 0.104 0.876 0.004 0.000 0.016
#> GSM152939 4 0.0870 0.94202 0.000 0.012 0.012 0.972 0.000 0.004
#> GSM152940 4 0.0000 0.94385 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152941 1 0.4079 0.25449 0.608 0.000 0.000 0.380 0.004 0.008
#> GSM152942 3 0.1829 0.74716 0.000 0.064 0.920 0.000 0.004 0.012
#> GSM152943 2 0.5624 0.45251 0.000 0.524 0.180 0.296 0.000 0.000
#> GSM152944 3 0.1088 0.73539 0.000 0.024 0.960 0.000 0.000 0.016
#> GSM152945 2 0.5385 -0.01103 0.000 0.500 0.420 0.052 0.000 0.028
#> GSM152946 2 0.1049 0.71184 0.000 0.960 0.008 0.032 0.000 0.000
#> GSM152947 4 0.0000 0.94385 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152948 2 0.3481 0.67885 0.000 0.776 0.000 0.032 0.000 0.192
#> GSM152949 3 0.3168 0.74003 0.000 0.172 0.804 0.000 0.000 0.024
#> GSM152950 3 0.4210 0.61037 0.000 0.336 0.636 0.000 0.000 0.028
#> GSM152951 2 0.2868 0.69343 0.000 0.840 0.000 0.028 0.000 0.132
#> GSM152952 2 0.3668 0.66930 0.000 0.744 0.000 0.028 0.000 0.228
#> GSM152953 2 0.3668 0.66930 0.000 0.744 0.000 0.028 0.000 0.228
#> GSM152954 4 0.0000 0.94385 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152955 3 0.6011 0.54441 0.000 0.308 0.532 0.036 0.000 0.124
#> GSM152956 2 0.3668 0.66930 0.000 0.744 0.000 0.028 0.000 0.228
#> GSM152957 4 0.0260 0.94524 0.000 0.008 0.000 0.992 0.000 0.000
#> GSM152958 4 0.0000 0.94385 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152959 4 0.0000 0.94385 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152960 4 0.2006 0.84959 0.000 0.104 0.004 0.892 0.000 0.000
#> GSM152961 4 0.0000 0.94385 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152962 3 0.4094 0.62652 0.000 0.324 0.652 0.000 0.000 0.024
#> GSM152963 2 0.3668 0.66930 0.000 0.744 0.000 0.028 0.000 0.228
#> GSM152964 5 0.7505 0.23653 0.004 0.096 0.292 0.036 0.448 0.124
#> GSM152965 2 0.2841 0.64975 0.000 0.824 0.164 0.012 0.000 0.000
#> GSM152966 4 0.0622 0.94413 0.000 0.012 0.008 0.980 0.000 0.000
#> GSM152967 2 0.0653 0.71069 0.000 0.980 0.004 0.012 0.000 0.004
#> GSM152968 3 0.4047 0.65149 0.000 0.296 0.676 0.000 0.000 0.028
#> GSM152969 4 0.0508 0.94489 0.000 0.012 0.004 0.984 0.000 0.000
#> GSM152970 4 0.0000 0.94385 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152971 4 0.0508 0.94489 0.000 0.012 0.004 0.984 0.000 0.000
#> GSM152972 4 0.0000 0.94385 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152973 4 0.3288 0.76240 0.000 0.016 0.176 0.800 0.000 0.008
#> GSM152974 2 0.0951 0.70634 0.000 0.968 0.020 0.004 0.000 0.008
#> GSM152975 2 0.3917 0.60757 0.000 0.752 0.204 0.032 0.000 0.012
#> GSM152976 4 0.0363 0.94505 0.000 0.012 0.000 0.988 0.000 0.000
#> GSM152977 4 0.0146 0.94330 0.000 0.000 0.004 0.996 0.000 0.000
#> GSM152978 4 0.0865 0.92385 0.000 0.036 0.000 0.964 0.000 0.000
#> GSM152979 3 0.1092 0.72295 0.000 0.020 0.960 0.000 0.000 0.020
#> GSM152980 2 0.4057 0.66728 0.000 0.764 0.108 0.124 0.000 0.004
#> GSM152981 5 0.1320 0.85709 0.000 0.000 0.036 0.000 0.948 0.016
#> GSM152982 4 0.0909 0.93874 0.000 0.020 0.012 0.968 0.000 0.000
#> GSM152983 4 0.0363 0.94505 0.000 0.012 0.000 0.988 0.000 0.000
#> GSM152984 4 0.5176 0.42016 0.000 0.108 0.288 0.600 0.000 0.004
#> GSM152985 4 0.1268 0.91322 0.036 0.000 0.000 0.952 0.004 0.008
#> GSM152986 4 0.0260 0.94524 0.000 0.008 0.000 0.992 0.000 0.000
#> GSM152987 1 0.3894 0.29401 0.664 0.000 0.000 0.324 0.004 0.008
#> GSM152988 4 0.1857 0.90684 0.000 0.028 0.044 0.924 0.000 0.004
#> GSM152989 4 0.0291 0.94212 0.000 0.000 0.000 0.992 0.004 0.004
#> GSM152990 3 0.1257 0.73168 0.000 0.028 0.952 0.000 0.000 0.020
#> GSM152991 3 0.5567 0.61311 0.000 0.272 0.560 0.004 0.000 0.164
#> GSM187524 1 0.0000 0.59097 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM187525 1 0.0000 0.59097 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM187526 1 0.0000 0.59097 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM187527 1 0.3634 -0.16417 0.644 0.000 0.000 0.000 0.000 0.356
#> GSM152856 6 0.3817 0.98120 0.432 0.000 0.000 0.000 0.000 0.568
#> GSM152857 1 0.5893 0.20132 0.540 0.000 0.016 0.172 0.000 0.272
#> GSM152858 1 0.2454 0.44619 0.840 0.000 0.000 0.000 0.000 0.160
#> GSM152859 1 0.0000 0.59097 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152860 1 0.0000 0.59097 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152861 6 0.3851 0.92470 0.460 0.000 0.000 0.000 0.000 0.540
#> GSM152862 1 0.0000 0.59097 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152863 1 0.3620 -0.16901 0.648 0.000 0.000 0.000 0.000 0.352
#> GSM152864 6 0.3817 0.98120 0.432 0.000 0.000 0.000 0.000 0.568
#> GSM152865 6 0.3867 0.84816 0.488 0.000 0.000 0.000 0.000 0.512
#> GSM152866 1 0.2854 0.35214 0.792 0.000 0.000 0.000 0.000 0.208
#> GSM152867 6 0.3817 0.98120 0.432 0.000 0.000 0.000 0.000 0.568
#> GSM152868 6 0.3817 0.98120 0.432 0.000 0.000 0.000 0.000 0.568
#> GSM152869 6 0.3817 0.98120 0.432 0.000 0.000 0.000 0.000 0.568
#> GSM152870 1 0.0000 0.59097 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152871 1 0.3515 -0.04414 0.676 0.000 0.000 0.000 0.000 0.324
#> GSM152872 1 0.1910 0.51313 0.892 0.000 0.000 0.000 0.000 0.108
#> GSM152873 6 0.3817 0.98120 0.432 0.000 0.000 0.000 0.000 0.568
#> GSM152874 6 0.3817 0.98120 0.432 0.000 0.000 0.000 0.000 0.568
#> GSM152875 1 0.3695 -0.29735 0.624 0.000 0.000 0.000 0.000 0.376
#> GSM152876 1 0.3647 -0.20964 0.640 0.000 0.000 0.000 0.000 0.360
#> GSM152877 6 0.3817 0.98120 0.432 0.000 0.000 0.000 0.000 0.568
#> GSM152878 6 0.3823 0.97450 0.436 0.000 0.000 0.000 0.000 0.564
#> GSM152879 6 0.3817 0.98120 0.432 0.000 0.000 0.000 0.000 0.568
#> GSM152880 6 0.3817 0.98120 0.432 0.000 0.000 0.000 0.000 0.568
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> SD:mclust 171 6.38e-29 2
#> SD:mclust 161 9.04e-32 3
#> SD:mclust 162 5.59e-33 4
#> SD:mclust 139 3.78e-27 5
#> SD:mclust 146 2.00e-29 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["SD", "NMF"]
# you can also extract it by
# res = res_list["SD:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'SD' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.926 0.933 0.971 0.4586 0.535 0.535
#> 3 3 0.640 0.757 0.885 0.4202 0.670 0.453
#> 4 4 0.562 0.591 0.788 0.1092 0.840 0.595
#> 5 5 0.549 0.576 0.745 0.0759 0.850 0.548
#> 6 6 0.604 0.555 0.726 0.0447 0.892 0.578
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.983 0.000 1.000
#> GSM152805 2 0.0000 0.983 0.000 1.000
#> GSM152806 2 0.0000 0.983 0.000 1.000
#> GSM152807 2 0.0000 0.983 0.000 1.000
#> GSM152808 2 0.0000 0.983 0.000 1.000
#> GSM152809 2 0.0000 0.983 0.000 1.000
#> GSM152810 1 0.9129 0.564 0.672 0.328
#> GSM152811 2 0.0000 0.983 0.000 1.000
#> GSM152812 2 0.0000 0.983 0.000 1.000
#> GSM152813 2 0.0000 0.983 0.000 1.000
#> GSM152814 2 0.0000 0.983 0.000 1.000
#> GSM152815 2 0.0000 0.983 0.000 1.000
#> GSM152816 2 0.0000 0.983 0.000 1.000
#> GSM152817 2 0.0000 0.983 0.000 1.000
#> GSM152818 2 0.0000 0.983 0.000 1.000
#> GSM152819 2 0.0000 0.983 0.000 1.000
#> GSM152820 2 0.0000 0.983 0.000 1.000
#> GSM152821 2 0.0000 0.983 0.000 1.000
#> GSM153115 1 0.1414 0.934 0.980 0.020
#> GSM153116 2 0.0000 0.983 0.000 1.000
#> GSM153117 2 0.0000 0.983 0.000 1.000
#> GSM153118 2 0.0000 0.983 0.000 1.000
#> GSM153119 2 0.0000 0.983 0.000 1.000
#> GSM153120 1 0.0000 0.946 1.000 0.000
#> GSM153121 2 0.0000 0.983 0.000 1.000
#> GSM153122 2 0.0000 0.983 0.000 1.000
#> GSM153123 2 0.0000 0.983 0.000 1.000
#> GSM153124 2 0.1414 0.964 0.020 0.980
#> GSM153125 1 0.9635 0.434 0.612 0.388
#> GSM153126 2 0.0000 0.983 0.000 1.000
#> GSM153127 2 0.0000 0.983 0.000 1.000
#> GSM153128 2 0.0000 0.983 0.000 1.000
#> GSM153129 2 0.0000 0.983 0.000 1.000
#> GSM153130 2 0.0000 0.983 0.000 1.000
#> GSM153131 2 0.0000 0.983 0.000 1.000
#> GSM153132 2 0.0000 0.983 0.000 1.000
#> GSM153133 2 0.0000 0.983 0.000 1.000
#> GSM153134 2 0.0000 0.983 0.000 1.000
#> GSM153135 2 0.0000 0.983 0.000 1.000
#> GSM153136 1 0.6712 0.793 0.824 0.176
#> GSM153137 1 0.8909 0.604 0.692 0.308
#> GSM153138 2 0.0000 0.983 0.000 1.000
#> GSM153139 2 0.0000 0.983 0.000 1.000
#> GSM153140 2 0.0000 0.983 0.000 1.000
#> GSM153141 2 0.0000 0.983 0.000 1.000
#> GSM153142 2 0.0000 0.983 0.000 1.000
#> GSM153143 2 0.0000 0.983 0.000 1.000
#> GSM153144 2 0.0000 0.983 0.000 1.000
#> GSM153145 2 0.0000 0.983 0.000 1.000
#> GSM153146 2 0.0000 0.983 0.000 1.000
#> GSM153147 2 0.0000 0.983 0.000 1.000
#> GSM153148 2 0.0000 0.983 0.000 1.000
#> GSM153149 2 0.0000 0.983 0.000 1.000
#> GSM153150 1 0.0000 0.946 1.000 0.000
#> GSM153151 2 0.0000 0.983 0.000 1.000
#> GSM153152 2 0.0000 0.983 0.000 1.000
#> GSM153153 2 0.0000 0.983 0.000 1.000
#> GSM153154 2 0.0000 0.983 0.000 1.000
#> GSM153155 2 0.0000 0.983 0.000 1.000
#> GSM153156 2 0.0000 0.983 0.000 1.000
#> GSM153157 2 0.0000 0.983 0.000 1.000
#> GSM153158 2 0.0000 0.983 0.000 1.000
#> GSM153159 2 0.0000 0.983 0.000 1.000
#> GSM153160 2 0.0000 0.983 0.000 1.000
#> GSM153161 2 0.0000 0.983 0.000 1.000
#> GSM153162 2 0.0000 0.983 0.000 1.000
#> GSM153163 2 0.0000 0.983 0.000 1.000
#> GSM153164 2 0.0000 0.983 0.000 1.000
#> GSM153165 2 0.0000 0.983 0.000 1.000
#> GSM153166 2 0.0000 0.983 0.000 1.000
#> GSM153167 2 0.0000 0.983 0.000 1.000
#> GSM153168 2 0.0000 0.983 0.000 1.000
#> GSM153169 2 0.0000 0.983 0.000 1.000
#> GSM153170 2 0.0000 0.983 0.000 1.000
#> GSM153171 1 0.0000 0.946 1.000 0.000
#> GSM153172 2 0.0000 0.983 0.000 1.000
#> GSM153173 2 0.0000 0.983 0.000 1.000
#> GSM153174 2 0.0000 0.983 0.000 1.000
#> GSM153175 1 0.9686 0.410 0.604 0.396
#> GSM153176 2 0.9460 0.384 0.364 0.636
#> GSM153177 2 0.0000 0.983 0.000 1.000
#> GSM152931 1 0.7219 0.765 0.800 0.200
#> GSM152932 2 0.0000 0.983 0.000 1.000
#> GSM152933 2 0.0000 0.983 0.000 1.000
#> GSM152934 2 0.9358 0.411 0.352 0.648
#> GSM152935 2 0.0000 0.983 0.000 1.000
#> GSM152936 1 0.0938 0.939 0.988 0.012
#> GSM152937 2 0.0938 0.972 0.012 0.988
#> GSM152938 2 0.0000 0.983 0.000 1.000
#> GSM152939 2 0.7745 0.689 0.228 0.772
#> GSM152940 1 0.0000 0.946 1.000 0.000
#> GSM152941 1 0.0000 0.946 1.000 0.000
#> GSM152942 2 0.0000 0.983 0.000 1.000
#> GSM152943 2 0.9944 0.080 0.456 0.544
#> GSM152944 2 0.0000 0.983 0.000 1.000
#> GSM152945 2 0.0376 0.980 0.004 0.996
#> GSM152946 2 0.0000 0.983 0.000 1.000
#> GSM152947 1 0.0000 0.946 1.000 0.000
#> GSM152948 2 0.0000 0.983 0.000 1.000
#> GSM152949 2 0.0000 0.983 0.000 1.000
#> GSM152950 2 0.0000 0.983 0.000 1.000
#> GSM152951 2 0.0000 0.983 0.000 1.000
#> GSM152952 2 0.0000 0.983 0.000 1.000
#> GSM152953 2 0.0000 0.983 0.000 1.000
#> GSM152954 1 0.1843 0.928 0.972 0.028
#> GSM152955 2 0.0000 0.983 0.000 1.000
#> GSM152956 2 0.0000 0.983 0.000 1.000
#> GSM152957 1 0.0000 0.946 1.000 0.000
#> GSM152958 1 0.0000 0.946 1.000 0.000
#> GSM152959 1 0.0000 0.946 1.000 0.000
#> GSM152960 1 0.4562 0.875 0.904 0.096
#> GSM152961 1 0.0000 0.946 1.000 0.000
#> GSM152962 2 0.0000 0.983 0.000 1.000
#> GSM152963 2 0.0000 0.983 0.000 1.000
#> GSM152964 2 0.6048 0.808 0.148 0.852
#> GSM152965 2 0.0000 0.983 0.000 1.000
#> GSM152966 1 0.9427 0.501 0.640 0.360
#> GSM152967 2 0.0000 0.983 0.000 1.000
#> GSM152968 2 0.0000 0.983 0.000 1.000
#> GSM152969 1 0.6048 0.824 0.852 0.148
#> GSM152970 1 0.0000 0.946 1.000 0.000
#> GSM152971 1 0.3879 0.893 0.924 0.076
#> GSM152972 1 0.0000 0.946 1.000 0.000
#> GSM152973 2 0.0672 0.976 0.008 0.992
#> GSM152974 2 0.0000 0.983 0.000 1.000
#> GSM152975 2 0.0000 0.983 0.000 1.000
#> GSM152976 1 0.3114 0.909 0.944 0.056
#> GSM152977 1 0.9248 0.543 0.660 0.340
#> GSM152978 1 0.0000 0.946 1.000 0.000
#> GSM152979 2 0.0000 0.983 0.000 1.000
#> GSM152980 2 0.0000 0.983 0.000 1.000
#> GSM152981 2 0.0000 0.983 0.000 1.000
#> GSM152982 2 0.3431 0.916 0.064 0.936
#> GSM152983 1 0.8813 0.617 0.700 0.300
#> GSM152984 2 0.0000 0.983 0.000 1.000
#> GSM152985 1 0.0000 0.946 1.000 0.000
#> GSM152986 1 0.0000 0.946 1.000 0.000
#> GSM152987 1 0.0000 0.946 1.000 0.000
#> GSM152988 2 0.1184 0.968 0.016 0.984
#> GSM152989 1 0.0000 0.946 1.000 0.000
#> GSM152990 2 0.0000 0.983 0.000 1.000
#> GSM152991 2 0.0000 0.983 0.000 1.000
#> GSM187524 1 0.0000 0.946 1.000 0.000
#> GSM187525 1 0.0000 0.946 1.000 0.000
#> GSM187526 1 0.0000 0.946 1.000 0.000
#> GSM187527 1 0.0000 0.946 1.000 0.000
#> GSM152856 1 0.0000 0.946 1.000 0.000
#> GSM152857 1 0.0000 0.946 1.000 0.000
#> GSM152858 1 0.0000 0.946 1.000 0.000
#> GSM152859 1 0.0000 0.946 1.000 0.000
#> GSM152860 1 0.0000 0.946 1.000 0.000
#> GSM152861 1 0.0000 0.946 1.000 0.000
#> GSM152862 1 0.0000 0.946 1.000 0.000
#> GSM152863 1 0.0000 0.946 1.000 0.000
#> GSM152864 1 0.0000 0.946 1.000 0.000
#> GSM152865 1 0.0000 0.946 1.000 0.000
#> GSM152866 1 0.0000 0.946 1.000 0.000
#> GSM152867 1 0.0000 0.946 1.000 0.000
#> GSM152868 1 0.0000 0.946 1.000 0.000
#> GSM152869 1 0.0000 0.946 1.000 0.000
#> GSM152870 1 0.0000 0.946 1.000 0.000
#> GSM152871 1 0.0000 0.946 1.000 0.000
#> GSM152872 1 0.0000 0.946 1.000 0.000
#> GSM152873 1 0.0000 0.946 1.000 0.000
#> GSM152874 1 0.0000 0.946 1.000 0.000
#> GSM152875 1 0.0000 0.946 1.000 0.000
#> GSM152876 1 0.0000 0.946 1.000 0.000
#> GSM152877 1 0.0000 0.946 1.000 0.000
#> GSM152878 1 0.0000 0.946 1.000 0.000
#> GSM152879 1 0.0000 0.946 1.000 0.000
#> GSM152880 1 0.0000 0.946 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.2537 0.8087 0.000 0.920 0.080
#> GSM152805 3 0.0000 0.8735 0.000 0.000 1.000
#> GSM152806 3 0.0892 0.8680 0.020 0.000 0.980
#> GSM152807 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM152808 3 0.1643 0.8561 0.044 0.000 0.956
#> GSM152809 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM152810 3 0.5216 0.6009 0.260 0.000 0.740
#> GSM152811 3 0.2261 0.8406 0.068 0.000 0.932
#> GSM152812 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM152813 2 0.1643 0.8210 0.000 0.956 0.044
#> GSM152814 2 0.2165 0.8139 0.000 0.936 0.064
#> GSM152815 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM152816 3 0.0424 0.8745 0.000 0.008 0.992
#> GSM152817 3 0.1860 0.8511 0.052 0.000 0.948
#> GSM152818 3 0.0592 0.8706 0.012 0.000 0.988
#> GSM152819 3 0.2066 0.8614 0.000 0.060 0.940
#> GSM152820 3 0.4291 0.7479 0.000 0.180 0.820
#> GSM152821 2 0.5098 0.6673 0.000 0.752 0.248
#> GSM153115 2 0.1411 0.8072 0.036 0.964 0.000
#> GSM153116 3 0.0747 0.8745 0.000 0.016 0.984
#> GSM153117 3 0.3038 0.8303 0.000 0.104 0.896
#> GSM153118 2 0.5650 0.5653 0.000 0.688 0.312
#> GSM153119 3 0.1643 0.8561 0.044 0.000 0.956
#> GSM153120 1 0.6045 0.5344 0.620 0.380 0.000
#> GSM153121 3 0.1860 0.8654 0.000 0.052 0.948
#> GSM153122 3 0.2448 0.8346 0.076 0.000 0.924
#> GSM153123 2 0.5733 0.5432 0.000 0.676 0.324
#> GSM153124 2 0.0424 0.8279 0.000 0.992 0.008
#> GSM153125 2 0.0747 0.8196 0.016 0.984 0.000
#> GSM153126 3 0.0000 0.8735 0.000 0.000 1.000
#> GSM153127 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM153128 3 0.1620 0.8704 0.024 0.012 0.964
#> GSM153129 3 0.6291 0.0738 0.000 0.468 0.532
#> GSM153130 3 0.0000 0.8735 0.000 0.000 1.000
#> GSM153131 3 0.1289 0.8724 0.000 0.032 0.968
#> GSM153132 3 0.4399 0.7402 0.000 0.188 0.812
#> GSM153133 2 0.5138 0.6614 0.000 0.748 0.252
#> GSM153134 2 0.6235 0.2712 0.000 0.564 0.436
#> GSM153135 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM153136 2 0.3482 0.7221 0.128 0.872 0.000
#> GSM153137 2 0.1031 0.8153 0.024 0.976 0.000
#> GSM153138 2 0.3752 0.7685 0.000 0.856 0.144
#> GSM153139 3 0.0892 0.8747 0.000 0.020 0.980
#> GSM153140 2 0.1529 0.8221 0.000 0.960 0.040
#> GSM153141 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM153142 3 0.0000 0.8735 0.000 0.000 1.000
#> GSM153143 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM153144 2 0.2165 0.8140 0.000 0.936 0.064
#> GSM153145 3 0.0592 0.8706 0.012 0.000 0.988
#> GSM153146 2 0.5058 0.6722 0.000 0.756 0.244
#> GSM153147 3 0.6267 0.1348 0.000 0.452 0.548
#> GSM153148 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM153149 2 0.6180 0.3316 0.000 0.584 0.416
#> GSM153150 1 0.5905 0.5918 0.648 0.352 0.000
#> GSM153151 3 0.5988 0.3959 0.000 0.368 0.632
#> GSM153152 2 0.6295 0.1496 0.000 0.528 0.472
#> GSM153153 2 0.5138 0.6619 0.000 0.748 0.252
#> GSM153154 3 0.1964 0.8634 0.000 0.056 0.944
#> GSM153155 2 0.4235 0.7419 0.000 0.824 0.176
#> GSM153156 3 0.0892 0.8747 0.000 0.020 0.980
#> GSM153157 3 0.0747 0.8694 0.016 0.000 0.984
#> GSM153158 3 0.1163 0.8731 0.000 0.028 0.972
#> GSM153159 3 0.0000 0.8735 0.000 0.000 1.000
#> GSM153160 3 0.0000 0.8735 0.000 0.000 1.000
#> GSM153161 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM153162 3 0.6286 0.0893 0.000 0.464 0.536
#> GSM153163 3 0.0000 0.8735 0.000 0.000 1.000
#> GSM153164 3 0.4178 0.7625 0.000 0.172 0.828
#> GSM153165 3 0.1411 0.8711 0.000 0.036 0.964
#> GSM153166 2 0.6192 0.3187 0.000 0.580 0.420
#> GSM153167 2 0.6045 0.4231 0.000 0.620 0.380
#> GSM153168 3 0.1643 0.8561 0.044 0.000 0.956
#> GSM153169 3 0.0000 0.8735 0.000 0.000 1.000
#> GSM153170 3 0.3482 0.8086 0.000 0.128 0.872
#> GSM153171 2 0.6267 -0.1001 0.452 0.548 0.000
#> GSM153172 2 0.2711 0.8028 0.000 0.912 0.088
#> GSM153173 3 0.0592 0.8746 0.000 0.012 0.988
#> GSM153174 2 0.5016 0.6777 0.000 0.760 0.240
#> GSM153175 2 0.0747 0.8196 0.016 0.984 0.000
#> GSM153176 3 0.3816 0.7736 0.148 0.000 0.852
#> GSM153177 2 0.6274 0.2064 0.000 0.544 0.456
#> GSM152931 2 0.1031 0.8153 0.024 0.976 0.000
#> GSM152932 2 0.4796 0.7001 0.000 0.780 0.220
#> GSM152933 3 0.6302 0.0252 0.000 0.480 0.520
#> GSM152934 2 0.9269 0.3793 0.184 0.508 0.308
#> GSM152935 3 0.2356 0.8543 0.000 0.072 0.928
#> GSM152936 2 0.2959 0.7509 0.100 0.900 0.000
#> GSM152937 3 0.2845 0.8450 0.068 0.012 0.920
#> GSM152938 3 0.1643 0.8686 0.000 0.044 0.956
#> GSM152939 2 0.0424 0.8237 0.008 0.992 0.000
#> GSM152940 1 0.5760 0.6340 0.672 0.328 0.000
#> GSM152941 1 0.2537 0.8971 0.920 0.080 0.000
#> GSM152942 3 0.2165 0.8596 0.000 0.064 0.936
#> GSM152943 2 0.4645 0.6757 0.176 0.816 0.008
#> GSM152944 3 0.1031 0.8738 0.000 0.024 0.976
#> GSM152945 3 0.2165 0.8583 0.000 0.064 0.936
#> GSM152946 2 0.0592 0.8282 0.000 0.988 0.012
#> GSM152947 1 0.3412 0.8684 0.876 0.124 0.000
#> GSM152948 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM152949 3 0.5397 0.5960 0.000 0.280 0.720
#> GSM152950 3 0.5178 0.6361 0.000 0.256 0.744
#> GSM152951 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM152952 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM152953 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM152954 2 0.5254 0.5120 0.264 0.736 0.000
#> GSM152955 3 0.0237 0.8741 0.000 0.004 0.996
#> GSM152956 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM152957 1 0.5431 0.6977 0.716 0.284 0.000
#> GSM152958 1 0.6302 0.2934 0.520 0.480 0.000
#> GSM152959 1 0.3551 0.8622 0.868 0.132 0.000
#> GSM152960 2 0.4842 0.5922 0.224 0.776 0.000
#> GSM152961 1 0.5859 0.6098 0.656 0.344 0.000
#> GSM152962 3 0.2625 0.8458 0.000 0.084 0.916
#> GSM152963 2 0.0000 0.8275 0.000 1.000 0.000
#> GSM152964 3 0.3752 0.7702 0.144 0.000 0.856
#> GSM152965 2 0.5216 0.6505 0.000 0.740 0.260
#> GSM152966 2 0.1031 0.8153 0.024 0.976 0.000
#> GSM152967 2 0.1753 0.8195 0.000 0.952 0.048
#> GSM152968 3 0.5098 0.6505 0.000 0.248 0.752
#> GSM152969 2 0.1529 0.8049 0.040 0.960 0.000
#> GSM152970 1 0.2796 0.8902 0.908 0.092 0.000
#> GSM152971 2 0.1529 0.8047 0.040 0.960 0.000
#> GSM152972 2 0.2625 0.7663 0.084 0.916 0.000
#> GSM152973 3 0.7013 0.1671 0.020 0.432 0.548
#> GSM152974 2 0.3752 0.7675 0.000 0.856 0.144
#> GSM152975 2 0.4842 0.6969 0.000 0.776 0.224
#> GSM152976 1 0.6231 0.7890 0.772 0.148 0.080
#> GSM152977 3 0.5656 0.6173 0.264 0.008 0.728
#> GSM152978 2 0.5397 0.4721 0.280 0.720 0.000
#> GSM152979 3 0.0592 0.8746 0.000 0.012 0.988
#> GSM152980 2 0.2625 0.8064 0.000 0.916 0.084
#> GSM152981 3 0.1289 0.8625 0.032 0.000 0.968
#> GSM152982 2 0.5366 0.7124 0.016 0.776 0.208
#> GSM152983 2 0.1529 0.8055 0.040 0.960 0.000
#> GSM152984 2 0.6307 0.0882 0.000 0.512 0.488
#> GSM152985 1 0.2261 0.9034 0.932 0.068 0.000
#> GSM152986 2 0.4931 0.5595 0.232 0.768 0.000
#> GSM152987 1 0.0424 0.9144 0.992 0.008 0.000
#> GSM152988 2 0.0592 0.8282 0.000 0.988 0.012
#> GSM152989 1 0.3482 0.8658 0.872 0.128 0.000
#> GSM152990 3 0.1163 0.8736 0.000 0.028 0.972
#> GSM152991 3 0.1289 0.8727 0.000 0.032 0.968
#> GSM187524 1 0.0000 0.9129 1.000 0.000 0.000
#> GSM187525 1 0.0000 0.9129 1.000 0.000 0.000
#> GSM187526 1 0.0000 0.9129 1.000 0.000 0.000
#> GSM187527 1 0.1163 0.9150 0.972 0.028 0.000
#> GSM152856 1 0.1964 0.9082 0.944 0.056 0.000
#> GSM152857 1 0.3551 0.7977 0.868 0.000 0.132
#> GSM152858 1 0.0000 0.9129 1.000 0.000 0.000
#> GSM152859 1 0.1163 0.8958 0.972 0.000 0.028
#> GSM152860 1 0.0000 0.9129 1.000 0.000 0.000
#> GSM152861 1 0.0892 0.9152 0.980 0.020 0.000
#> GSM152862 1 0.0000 0.9129 1.000 0.000 0.000
#> GSM152863 1 0.0424 0.9086 0.992 0.000 0.008
#> GSM152864 1 0.1411 0.9137 0.964 0.036 0.000
#> GSM152865 1 0.0000 0.9129 1.000 0.000 0.000
#> GSM152866 1 0.0000 0.9129 1.000 0.000 0.000
#> GSM152867 1 0.1860 0.9097 0.948 0.052 0.000
#> GSM152868 1 0.1964 0.9082 0.944 0.056 0.000
#> GSM152869 1 0.1860 0.9097 0.948 0.052 0.000
#> GSM152870 1 0.0000 0.9129 1.000 0.000 0.000
#> GSM152871 1 0.0000 0.9129 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.9129 1.000 0.000 0.000
#> GSM152873 1 0.0237 0.9137 0.996 0.004 0.000
#> GSM152874 1 0.0424 0.9144 0.992 0.008 0.000
#> GSM152875 1 0.0000 0.9129 1.000 0.000 0.000
#> GSM152876 1 0.1289 0.9144 0.968 0.032 0.000
#> GSM152877 1 0.1031 0.9152 0.976 0.024 0.000
#> GSM152878 1 0.1529 0.9129 0.960 0.040 0.000
#> GSM152879 1 0.1643 0.9119 0.956 0.044 0.000
#> GSM152880 1 0.1031 0.9152 0.976 0.024 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.6682 0.5174 0.032 0.612 0.304 0.052
#> GSM152805 3 0.4277 0.4903 0.000 0.000 0.720 0.280
#> GSM152806 3 0.4955 0.2258 0.000 0.000 0.556 0.444
#> GSM152807 2 0.0895 0.8487 0.000 0.976 0.004 0.020
#> GSM152808 3 0.4977 0.1889 0.000 0.000 0.540 0.460
#> GSM152809 2 0.0657 0.8483 0.000 0.984 0.004 0.012
#> GSM152810 4 0.3652 0.5167 0.052 0.000 0.092 0.856
#> GSM152811 3 0.5295 0.0415 0.008 0.000 0.504 0.488
#> GSM152812 2 0.0336 0.8481 0.000 0.992 0.000 0.008
#> GSM152813 2 0.3100 0.8351 0.004 0.888 0.080 0.028
#> GSM152814 2 0.2973 0.8285 0.000 0.884 0.096 0.020
#> GSM152815 2 0.0000 0.8474 0.000 1.000 0.000 0.000
#> GSM152816 3 0.3539 0.5834 0.000 0.004 0.820 0.176
#> GSM152817 3 0.4998 0.1074 0.000 0.000 0.512 0.488
#> GSM152818 3 0.4643 0.4093 0.000 0.000 0.656 0.344
#> GSM152819 3 0.5773 0.4312 0.000 0.048 0.632 0.320
#> GSM152820 3 0.6695 0.4268 0.000 0.164 0.616 0.220
#> GSM152821 2 0.2399 0.8387 0.000 0.920 0.048 0.032
#> GSM153115 1 0.8884 0.2804 0.452 0.240 0.236 0.072
#> GSM153116 3 0.5329 0.2900 0.000 0.012 0.568 0.420
#> GSM153117 3 0.5489 0.4756 0.000 0.040 0.664 0.296
#> GSM153118 2 0.3320 0.8193 0.000 0.876 0.068 0.056
#> GSM153119 4 0.4964 0.2276 0.000 0.004 0.380 0.616
#> GSM153120 2 0.5383 0.6605 0.100 0.740 0.000 0.160
#> GSM153121 3 0.0672 0.6205 0.000 0.008 0.984 0.008
#> GSM153122 4 0.5279 0.2161 0.012 0.000 0.400 0.588
#> GSM153123 2 0.5062 0.6455 0.000 0.692 0.284 0.024
#> GSM153124 2 0.6425 0.6146 0.032 0.640 0.284 0.044
#> GSM153125 2 0.4644 0.8014 0.064 0.828 0.068 0.040
#> GSM153126 3 0.0779 0.6136 0.004 0.000 0.980 0.016
#> GSM153127 2 0.0336 0.8476 0.000 0.992 0.000 0.008
#> GSM153128 4 0.4332 0.4925 0.000 0.032 0.176 0.792
#> GSM153129 3 0.3757 0.5301 0.000 0.152 0.828 0.020
#> GSM153130 3 0.1716 0.6270 0.000 0.000 0.936 0.064
#> GSM153131 3 0.3591 0.5964 0.000 0.008 0.824 0.168
#> GSM153132 3 0.6617 0.4437 0.000 0.176 0.628 0.196
#> GSM153133 2 0.3616 0.8148 0.000 0.852 0.112 0.036
#> GSM153134 3 0.4446 0.4929 0.000 0.196 0.776 0.028
#> GSM153135 2 0.0000 0.8474 0.000 1.000 0.000 0.000
#> GSM153136 2 0.4872 0.6804 0.212 0.752 0.004 0.032
#> GSM153137 2 0.1042 0.8438 0.008 0.972 0.000 0.020
#> GSM153138 2 0.2334 0.8271 0.000 0.908 0.004 0.088
#> GSM153139 3 0.2611 0.6263 0.000 0.008 0.896 0.096
#> GSM153140 2 0.3027 0.8333 0.004 0.888 0.088 0.020
#> GSM153141 2 0.0000 0.8474 0.000 1.000 0.000 0.000
#> GSM153142 3 0.4830 0.3397 0.000 0.000 0.608 0.392
#> GSM153143 2 0.0336 0.8486 0.000 0.992 0.008 0.000
#> GSM153144 2 0.5055 0.6878 0.000 0.712 0.256 0.032
#> GSM153145 3 0.4992 0.1440 0.000 0.000 0.524 0.476
#> GSM153146 2 0.2002 0.8418 0.000 0.936 0.020 0.044
#> GSM153147 3 0.4332 0.4832 0.000 0.176 0.792 0.032
#> GSM153148 2 0.0336 0.8486 0.000 0.992 0.008 0.000
#> GSM153149 2 0.4100 0.7839 0.000 0.824 0.128 0.048
#> GSM153150 2 0.6016 0.5669 0.208 0.680 0.000 0.112
#> GSM153151 2 0.6996 0.4951 0.000 0.580 0.192 0.228
#> GSM153152 2 0.5937 0.1498 0.000 0.492 0.472 0.036
#> GSM153153 2 0.2546 0.8356 0.000 0.912 0.060 0.028
#> GSM153154 3 0.4453 0.5416 0.000 0.012 0.744 0.244
#> GSM153155 2 0.2142 0.8425 0.000 0.928 0.056 0.016
#> GSM153156 3 0.2125 0.6258 0.000 0.004 0.920 0.076
#> GSM153157 3 0.4992 0.1267 0.000 0.000 0.524 0.476
#> GSM153158 3 0.4877 0.4443 0.000 0.008 0.664 0.328
#> GSM153159 3 0.4776 0.3682 0.000 0.000 0.624 0.376
#> GSM153160 3 0.0779 0.6164 0.004 0.000 0.980 0.016
#> GSM153161 2 0.0188 0.8475 0.000 0.996 0.000 0.004
#> GSM153162 3 0.2313 0.5937 0.000 0.032 0.924 0.044
#> GSM153163 3 0.2466 0.6240 0.000 0.004 0.900 0.096
#> GSM153164 3 0.7719 0.1986 0.000 0.268 0.448 0.284
#> GSM153165 3 0.1356 0.6060 0.000 0.008 0.960 0.032
#> GSM153166 3 0.5781 -0.0357 0.000 0.484 0.488 0.028
#> GSM153167 3 0.5611 0.1174 0.000 0.412 0.564 0.024
#> GSM153168 4 0.4998 -0.1036 0.000 0.000 0.488 0.512
#> GSM153169 3 0.2714 0.6210 0.000 0.004 0.884 0.112
#> GSM153170 3 0.1297 0.6216 0.000 0.020 0.964 0.016
#> GSM153171 1 0.6453 0.4490 0.608 0.324 0.024 0.044
#> GSM153172 2 0.1398 0.8471 0.000 0.956 0.040 0.004
#> GSM153173 3 0.0927 0.6244 0.000 0.008 0.976 0.016
#> GSM153174 3 0.6000 0.1793 0.000 0.356 0.592 0.052
#> GSM153175 1 0.7789 0.3573 0.552 0.072 0.296 0.080
#> GSM153176 3 0.4139 0.4462 0.144 0.000 0.816 0.040
#> GSM153177 2 0.5496 0.6317 0.000 0.704 0.232 0.064
#> GSM152931 2 0.5154 0.7762 0.060 0.796 0.104 0.040
#> GSM152932 2 0.3099 0.8169 0.000 0.876 0.104 0.020
#> GSM152933 2 0.6193 0.5949 0.000 0.672 0.180 0.148
#> GSM152934 2 0.6320 0.4406 0.012 0.576 0.044 0.368
#> GSM152935 4 0.7722 0.0473 0.000 0.256 0.300 0.444
#> GSM152936 2 0.1284 0.8420 0.024 0.964 0.000 0.012
#> GSM152937 4 0.5345 0.4043 0.016 0.012 0.292 0.680
#> GSM152938 3 0.3166 0.6111 0.000 0.016 0.868 0.116
#> GSM152939 1 0.9215 0.1278 0.348 0.260 0.316 0.076
#> GSM152940 2 0.6646 0.4635 0.224 0.620 0.000 0.156
#> GSM152941 1 0.5565 0.6819 0.700 0.068 0.000 0.232
#> GSM152942 3 0.1082 0.6110 0.004 0.004 0.972 0.020
#> GSM152943 2 0.4896 0.6215 0.012 0.704 0.004 0.280
#> GSM152944 3 0.2944 0.6142 0.000 0.004 0.868 0.128
#> GSM152945 4 0.4604 0.4484 0.008 0.180 0.028 0.784
#> GSM152946 2 0.1890 0.8469 0.000 0.936 0.056 0.008
#> GSM152947 1 0.7133 0.5174 0.548 0.172 0.000 0.280
#> GSM152948 2 0.1042 0.8489 0.000 0.972 0.008 0.020
#> GSM152949 3 0.1520 0.6110 0.000 0.024 0.956 0.020
#> GSM152950 3 0.5932 0.4422 0.000 0.224 0.680 0.096
#> GSM152951 2 0.0672 0.8491 0.000 0.984 0.008 0.008
#> GSM152952 2 0.0188 0.8475 0.000 0.996 0.000 0.004
#> GSM152953 2 0.0657 0.8485 0.000 0.984 0.004 0.012
#> GSM152954 2 0.3707 0.7852 0.112 0.852 0.004 0.032
#> GSM152955 4 0.5723 0.4012 0.000 0.072 0.244 0.684
#> GSM152956 2 0.0336 0.8486 0.000 0.992 0.008 0.000
#> GSM152957 1 0.3743 0.7197 0.864 0.012 0.080 0.044
#> GSM152958 2 0.5169 0.5554 0.272 0.696 0.000 0.032
#> GSM152959 1 0.5537 0.7011 0.720 0.056 0.008 0.216
#> GSM152960 2 0.2255 0.8244 0.012 0.920 0.000 0.068
#> GSM152961 1 0.5282 0.5546 0.688 0.276 0.000 0.036
#> GSM152962 3 0.7172 0.1455 0.000 0.140 0.484 0.376
#> GSM152963 2 0.0469 0.8478 0.000 0.988 0.000 0.012
#> GSM152964 4 0.2915 0.5185 0.028 0.000 0.080 0.892
#> GSM152965 2 0.2142 0.8388 0.000 0.928 0.016 0.056
#> GSM152966 2 0.5806 0.7447 0.112 0.756 0.092 0.040
#> GSM152967 2 0.2021 0.8452 0.000 0.932 0.056 0.012
#> GSM152968 3 0.2996 0.6141 0.000 0.064 0.892 0.044
#> GSM152969 2 0.1059 0.8456 0.012 0.972 0.000 0.016
#> GSM152970 1 0.4640 0.7312 0.776 0.032 0.004 0.188
#> GSM152971 2 0.3283 0.8290 0.044 0.892 0.044 0.020
#> GSM152972 2 0.1388 0.8403 0.028 0.960 0.000 0.012
#> GSM152973 3 0.6575 -0.0478 0.412 0.000 0.508 0.080
#> GSM152974 2 0.2799 0.8249 0.000 0.884 0.108 0.008
#> GSM152975 2 0.3617 0.8095 0.000 0.860 0.076 0.064
#> GSM152976 1 0.3722 0.7304 0.868 0.016 0.044 0.072
#> GSM152977 4 0.7074 0.4419 0.192 0.000 0.240 0.568
#> GSM152978 2 0.2443 0.8177 0.024 0.916 0.000 0.060
#> GSM152979 3 0.2334 0.6266 0.000 0.004 0.908 0.088
#> GSM152980 2 0.1488 0.8467 0.000 0.956 0.012 0.032
#> GSM152981 4 0.4888 0.1495 0.000 0.000 0.412 0.588
#> GSM152982 2 0.6188 0.5203 0.012 0.596 0.352 0.040
#> GSM152983 2 0.2673 0.8327 0.048 0.916 0.020 0.016
#> GSM152984 3 0.2409 0.5931 0.004 0.032 0.924 0.040
#> GSM152985 1 0.6270 0.5039 0.536 0.060 0.000 0.404
#> GSM152986 2 0.6096 0.3095 0.376 0.576 0.004 0.044
#> GSM152987 4 0.5861 -0.4330 0.476 0.032 0.000 0.492
#> GSM152988 1 0.7599 0.2272 0.476 0.036 0.400 0.088
#> GSM152989 1 0.2300 0.7782 0.924 0.028 0.000 0.048
#> GSM152990 3 0.1284 0.6264 0.000 0.012 0.964 0.024
#> GSM152991 4 0.6554 0.0534 0.000 0.080 0.400 0.520
#> GSM187524 1 0.5168 0.3943 0.500 0.004 0.000 0.496
#> GSM187525 1 0.5478 0.4793 0.540 0.016 0.000 0.444
#> GSM187526 1 0.4158 0.7184 0.768 0.008 0.000 0.224
#> GSM187527 1 0.0895 0.7765 0.976 0.000 0.004 0.020
#> GSM152856 1 0.0927 0.7795 0.976 0.008 0.000 0.016
#> GSM152857 1 0.3245 0.7281 0.872 0.000 0.028 0.100
#> GSM152858 1 0.3539 0.7418 0.820 0.000 0.004 0.176
#> GSM152859 4 0.5244 -0.3330 0.436 0.000 0.008 0.556
#> GSM152860 1 0.4720 0.6389 0.672 0.004 0.000 0.324
#> GSM152861 1 0.2053 0.7777 0.924 0.004 0.000 0.072
#> GSM152862 1 0.4697 0.6066 0.644 0.000 0.000 0.356
#> GSM152863 1 0.1677 0.7814 0.948 0.000 0.012 0.040
#> GSM152864 1 0.0188 0.7811 0.996 0.004 0.000 0.000
#> GSM152865 1 0.1661 0.7801 0.944 0.000 0.004 0.052
#> GSM152866 1 0.3610 0.7324 0.800 0.000 0.000 0.200
#> GSM152867 1 0.0817 0.7757 0.976 0.000 0.000 0.024
#> GSM152868 1 0.1004 0.7752 0.972 0.000 0.004 0.024
#> GSM152869 1 0.0188 0.7804 0.996 0.000 0.000 0.004
#> GSM152870 1 0.4790 0.5802 0.620 0.000 0.000 0.380
#> GSM152871 1 0.2334 0.7727 0.908 0.000 0.004 0.088
#> GSM152872 1 0.3870 0.7271 0.788 0.000 0.004 0.208
#> GSM152873 1 0.0592 0.7821 0.984 0.000 0.000 0.016
#> GSM152874 1 0.1211 0.7816 0.960 0.000 0.000 0.040
#> GSM152875 1 0.0592 0.7823 0.984 0.000 0.000 0.016
#> GSM152876 1 0.1970 0.7603 0.932 0.000 0.008 0.060
#> GSM152877 1 0.1398 0.7827 0.956 0.004 0.000 0.040
#> GSM152878 1 0.0469 0.7784 0.988 0.000 0.000 0.012
#> GSM152879 1 0.0657 0.7819 0.984 0.004 0.000 0.012
#> GSM152880 1 0.1452 0.7833 0.956 0.008 0.000 0.036
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.7437 0.4977 0.052 0.580 0.132 0.048 0.188
#> GSM152805 5 0.1597 0.7610 0.000 0.000 0.048 0.012 0.940
#> GSM152806 5 0.0798 0.7731 0.000 0.000 0.016 0.008 0.976
#> GSM152807 2 0.2095 0.7673 0.008 0.920 0.012 0.060 0.000
#> GSM152808 5 0.0807 0.7732 0.000 0.000 0.012 0.012 0.976
#> GSM152809 2 0.1788 0.7684 0.008 0.932 0.004 0.056 0.000
#> GSM152810 4 0.5824 0.3214 0.036 0.000 0.040 0.568 0.356
#> GSM152811 5 0.1670 0.7682 0.000 0.000 0.012 0.052 0.936
#> GSM152812 2 0.1856 0.7690 0.008 0.936 0.008 0.044 0.004
#> GSM152813 2 0.2593 0.7686 0.004 0.904 0.048 0.036 0.008
#> GSM152814 2 0.3373 0.7546 0.008 0.868 0.016 0.052 0.056
#> GSM152815 2 0.1931 0.7680 0.008 0.932 0.008 0.048 0.004
#> GSM152816 5 0.4497 0.6581 0.000 0.072 0.136 0.016 0.776
#> GSM152817 5 0.0579 0.7740 0.000 0.000 0.008 0.008 0.984
#> GSM152818 5 0.0963 0.7676 0.000 0.000 0.036 0.000 0.964
#> GSM152819 5 0.4140 0.6943 0.004 0.152 0.032 0.016 0.796
#> GSM152820 5 0.4751 0.6557 0.000 0.172 0.044 0.032 0.752
#> GSM152821 2 0.3938 0.6843 0.000 0.796 0.016 0.024 0.164
#> GSM153115 3 0.7977 0.1501 0.252 0.184 0.436 0.128 0.000
#> GSM153116 5 0.2011 0.7673 0.000 0.044 0.020 0.008 0.928
#> GSM153117 5 0.3525 0.7260 0.000 0.120 0.032 0.012 0.836
#> GSM153118 2 0.3583 0.6922 0.000 0.808 0.008 0.016 0.168
#> GSM153119 5 0.3106 0.7068 0.000 0.000 0.020 0.140 0.840
#> GSM153120 2 0.5784 0.4609 0.048 0.576 0.028 0.348 0.000
#> GSM153121 3 0.4179 0.6738 0.000 0.016 0.756 0.016 0.212
#> GSM153122 5 0.6133 0.2493 0.004 0.000 0.120 0.364 0.512
#> GSM153123 2 0.5477 0.3399 0.000 0.584 0.360 0.032 0.024
#> GSM153124 3 0.5581 0.4458 0.004 0.228 0.656 0.108 0.004
#> GSM153125 2 0.6545 0.5957 0.064 0.620 0.140 0.176 0.000
#> GSM153126 3 0.3724 0.6706 0.000 0.000 0.776 0.020 0.204
#> GSM153127 2 0.1186 0.7719 0.000 0.964 0.008 0.020 0.008
#> GSM153128 4 0.7261 0.3700 0.000 0.116 0.136 0.552 0.196
#> GSM153129 3 0.5416 0.6680 0.000 0.116 0.688 0.012 0.184
#> GSM153130 3 0.4574 0.4431 0.000 0.000 0.576 0.012 0.412
#> GSM153131 5 0.5600 0.1599 0.000 0.052 0.348 0.016 0.584
#> GSM153132 5 0.5036 0.5997 0.000 0.208 0.064 0.016 0.712
#> GSM153133 2 0.4103 0.7241 0.000 0.800 0.132 0.056 0.012
#> GSM153134 3 0.6999 0.4073 0.000 0.280 0.456 0.016 0.248
#> GSM153135 2 0.0510 0.7717 0.000 0.984 0.000 0.016 0.000
#> GSM153136 2 0.7092 0.5235 0.132 0.572 0.108 0.188 0.000
#> GSM153137 2 0.2354 0.7632 0.008 0.904 0.012 0.076 0.000
#> GSM153138 2 0.2959 0.7499 0.000 0.864 0.016 0.112 0.008
#> GSM153139 3 0.5543 0.3295 0.000 0.036 0.500 0.016 0.448
#> GSM153140 2 0.4369 0.7410 0.012 0.804 0.092 0.080 0.012
#> GSM153141 2 0.1026 0.7711 0.004 0.968 0.004 0.024 0.000
#> GSM153142 5 0.0771 0.7729 0.000 0.000 0.020 0.004 0.976
#> GSM153143 2 0.1608 0.7661 0.000 0.928 0.000 0.072 0.000
#> GSM153144 2 0.4110 0.6054 0.000 0.736 0.244 0.008 0.012
#> GSM153145 5 0.1211 0.7720 0.000 0.000 0.016 0.024 0.960
#> GSM153146 2 0.2633 0.7519 0.000 0.896 0.012 0.024 0.068
#> GSM153147 3 0.4876 0.6865 0.000 0.096 0.756 0.024 0.124
#> GSM153148 2 0.0727 0.7716 0.000 0.980 0.004 0.012 0.004
#> GSM153149 2 0.3654 0.7379 0.000 0.848 0.048 0.036 0.068
#> GSM153150 2 0.6145 0.2344 0.052 0.472 0.036 0.440 0.000
#> GSM153151 2 0.7616 0.1604 0.000 0.408 0.256 0.284 0.052
#> GSM153152 2 0.6364 -0.1061 0.000 0.452 0.436 0.024 0.088
#> GSM153153 2 0.3775 0.7038 0.000 0.812 0.024 0.016 0.148
#> GSM153154 5 0.3776 0.6881 0.000 0.040 0.128 0.012 0.820
#> GSM153155 2 0.2201 0.7694 0.000 0.920 0.040 0.032 0.008
#> GSM153156 3 0.4878 0.6543 0.000 0.028 0.700 0.024 0.248
#> GSM153157 5 0.2054 0.7613 0.000 0.000 0.028 0.052 0.920
#> GSM153158 5 0.1564 0.7726 0.000 0.024 0.024 0.004 0.948
#> GSM153159 5 0.1741 0.7707 0.000 0.000 0.040 0.024 0.936
#> GSM153160 3 0.3596 0.6728 0.000 0.000 0.784 0.016 0.200
#> GSM153161 2 0.1408 0.7714 0.000 0.948 0.008 0.044 0.000
#> GSM153162 3 0.4535 0.6871 0.000 0.040 0.756 0.020 0.184
#> GSM153163 5 0.4852 0.2450 0.000 0.012 0.348 0.016 0.624
#> GSM153164 5 0.4156 0.6681 0.000 0.168 0.028 0.020 0.784
#> GSM153165 3 0.4405 0.6253 0.000 0.004 0.696 0.020 0.280
#> GSM153166 2 0.6443 0.3136 0.000 0.552 0.136 0.020 0.292
#> GSM153167 3 0.6140 0.5651 0.000 0.260 0.608 0.028 0.104
#> GSM153168 5 0.1168 0.7698 0.000 0.000 0.008 0.032 0.960
#> GSM153169 3 0.4954 0.5116 0.000 0.012 0.592 0.016 0.380
#> GSM153170 3 0.4616 0.6299 0.000 0.028 0.680 0.004 0.288
#> GSM153171 3 0.7536 0.1903 0.152 0.108 0.504 0.236 0.000
#> GSM153172 2 0.1483 0.7721 0.000 0.952 0.028 0.012 0.008
#> GSM153173 3 0.4552 0.5436 0.000 0.004 0.632 0.012 0.352
#> GSM153174 3 0.4072 0.6602 0.000 0.152 0.792 0.008 0.048
#> GSM153175 3 0.4366 0.5861 0.088 0.044 0.804 0.064 0.000
#> GSM153176 3 0.3816 0.6724 0.016 0.000 0.828 0.056 0.100
#> GSM153177 2 0.4543 0.6739 0.000 0.768 0.048 0.024 0.160
#> GSM152931 2 0.7009 0.4887 0.044 0.520 0.272 0.164 0.000
#> GSM152932 2 0.3184 0.7499 0.000 0.872 0.068 0.032 0.028
#> GSM152933 5 0.5266 0.0937 0.000 0.468 0.016 0.020 0.496
#> GSM152934 4 0.5903 0.3188 0.000 0.272 0.108 0.608 0.012
#> GSM152935 5 0.7608 0.2169 0.000 0.268 0.096 0.160 0.476
#> GSM152936 2 0.5642 0.6094 0.000 0.624 0.136 0.240 0.000
#> GSM152937 4 0.7066 0.1488 0.012 0.044 0.352 0.492 0.100
#> GSM152938 3 0.5154 0.6737 0.004 0.032 0.744 0.080 0.140
#> GSM152939 3 0.3898 0.6108 0.044 0.084 0.832 0.040 0.000
#> GSM152940 4 0.5877 0.2481 0.036 0.316 0.052 0.596 0.000
#> GSM152941 4 0.5938 0.2374 0.360 0.028 0.056 0.556 0.000
#> GSM152942 3 0.3093 0.6827 0.000 0.000 0.824 0.008 0.168
#> GSM152943 4 0.5405 0.0603 0.000 0.380 0.064 0.556 0.000
#> GSM152944 5 0.3989 0.4914 0.000 0.008 0.260 0.004 0.728
#> GSM152945 4 0.7333 0.4382 0.020 0.148 0.068 0.572 0.192
#> GSM152946 2 0.5053 0.6623 0.000 0.688 0.216 0.096 0.000
#> GSM152947 4 0.6086 0.4924 0.100 0.040 0.200 0.656 0.004
#> GSM152948 2 0.1012 0.7740 0.000 0.968 0.012 0.020 0.000
#> GSM152949 3 0.4646 0.6791 0.000 0.044 0.732 0.012 0.212
#> GSM152950 3 0.7198 0.4508 0.000 0.204 0.484 0.040 0.272
#> GSM152951 2 0.1018 0.7735 0.000 0.968 0.016 0.016 0.000
#> GSM152952 2 0.1026 0.7710 0.000 0.968 0.004 0.024 0.004
#> GSM152953 2 0.1202 0.7705 0.000 0.960 0.004 0.032 0.004
#> GSM152954 2 0.6529 0.5426 0.060 0.588 0.092 0.260 0.000
#> GSM152955 5 0.5008 0.4718 0.000 0.024 0.024 0.284 0.668
#> GSM152956 2 0.0671 0.7729 0.000 0.980 0.004 0.016 0.000
#> GSM152957 3 0.5624 0.3888 0.176 0.020 0.680 0.124 0.000
#> GSM152958 2 0.6421 0.5672 0.076 0.616 0.080 0.228 0.000
#> GSM152959 4 0.6166 0.4515 0.164 0.048 0.136 0.652 0.000
#> GSM152960 2 0.4146 0.6566 0.004 0.716 0.012 0.268 0.000
#> GSM152961 1 0.7882 -0.0845 0.360 0.316 0.072 0.252 0.000
#> GSM152962 3 0.8529 0.1712 0.000 0.208 0.320 0.240 0.232
#> GSM152963 2 0.1153 0.7711 0.000 0.964 0.008 0.024 0.004
#> GSM152964 4 0.5579 0.2586 0.020 0.004 0.032 0.572 0.372
#> GSM152965 2 0.3579 0.7470 0.000 0.836 0.032 0.116 0.016
#> GSM152966 2 0.7341 0.5147 0.112 0.544 0.180 0.164 0.000
#> GSM152967 2 0.1701 0.7741 0.000 0.944 0.028 0.016 0.012
#> GSM152968 3 0.6081 0.5694 0.000 0.104 0.580 0.016 0.300
#> GSM152969 2 0.5359 0.6517 0.012 0.688 0.100 0.200 0.000
#> GSM152970 4 0.6582 0.3770 0.232 0.012 0.220 0.536 0.000
#> GSM152971 2 0.5632 0.6415 0.016 0.676 0.144 0.164 0.000
#> GSM152972 2 0.4588 0.6726 0.004 0.736 0.060 0.200 0.000
#> GSM152973 3 0.3545 0.6337 0.100 0.004 0.848 0.020 0.028
#> GSM152974 2 0.2778 0.7620 0.000 0.892 0.060 0.032 0.016
#> GSM152975 2 0.5787 0.5350 0.000 0.608 0.020 0.072 0.300
#> GSM152976 3 0.7019 -0.0125 0.388 0.012 0.416 0.176 0.008
#> GSM152977 4 0.6828 0.3620 0.044 0.012 0.088 0.544 0.312
#> GSM152978 2 0.4970 0.6207 0.016 0.672 0.032 0.280 0.000
#> GSM152979 3 0.4540 0.6143 0.000 0.016 0.676 0.008 0.300
#> GSM152980 2 0.3497 0.7539 0.000 0.836 0.048 0.112 0.004
#> GSM152981 5 0.2669 0.7299 0.000 0.000 0.020 0.104 0.876
#> GSM152982 3 0.5676 0.4478 0.000 0.120 0.644 0.228 0.008
#> GSM152983 2 0.6533 0.4671 0.004 0.512 0.240 0.244 0.000
#> GSM152984 3 0.2938 0.6886 0.000 0.032 0.876 0.008 0.084
#> GSM152985 4 0.4726 0.5009 0.112 0.032 0.064 0.784 0.008
#> GSM152986 2 0.7618 0.4150 0.184 0.504 0.116 0.196 0.000
#> GSM152987 4 0.5075 0.4660 0.220 0.020 0.028 0.716 0.016
#> GSM152988 3 0.3812 0.5892 0.136 0.016 0.816 0.032 0.000
#> GSM152989 1 0.5958 0.2362 0.524 0.004 0.100 0.372 0.000
#> GSM152990 3 0.4509 0.6676 0.000 0.024 0.728 0.016 0.232
#> GSM152991 5 0.3648 0.7343 0.000 0.096 0.020 0.044 0.840
#> GSM187524 4 0.4433 0.3934 0.280 0.000 0.008 0.696 0.016
#> GSM187525 4 0.4438 0.2974 0.340 0.004 0.004 0.648 0.004
#> GSM187526 1 0.4607 0.3971 0.616 0.000 0.012 0.368 0.004
#> GSM187527 1 0.1117 0.7867 0.964 0.000 0.020 0.016 0.000
#> GSM152856 1 0.1153 0.7837 0.964 0.008 0.004 0.024 0.000
#> GSM152857 1 0.2403 0.7316 0.904 0.000 0.012 0.012 0.072
#> GSM152858 1 0.5420 0.2884 0.548 0.000 0.052 0.396 0.004
#> GSM152859 4 0.5246 0.3844 0.272 0.000 0.040 0.664 0.024
#> GSM152860 4 0.5368 -0.0908 0.472 0.000 0.036 0.484 0.008
#> GSM152861 1 0.3488 0.7076 0.808 0.000 0.024 0.168 0.000
#> GSM152862 4 0.5362 -0.0377 0.456 0.000 0.036 0.500 0.008
#> GSM152863 1 0.2520 0.7837 0.896 0.000 0.048 0.056 0.000
#> GSM152864 1 0.1568 0.7954 0.944 0.000 0.020 0.036 0.000
#> GSM152865 1 0.2951 0.7525 0.860 0.000 0.028 0.112 0.000
#> GSM152866 1 0.3934 0.5910 0.740 0.000 0.016 0.244 0.000
#> GSM152867 1 0.1471 0.7826 0.952 0.004 0.020 0.024 0.000
#> GSM152868 1 0.1828 0.7889 0.936 0.004 0.032 0.028 0.000
#> GSM152869 1 0.1668 0.7930 0.940 0.000 0.032 0.028 0.000
#> GSM152870 4 0.5349 0.0123 0.440 0.000 0.036 0.516 0.008
#> GSM152871 1 0.4706 0.5811 0.692 0.000 0.052 0.256 0.000
#> GSM152872 1 0.5481 0.2765 0.544 0.000 0.048 0.400 0.008
#> GSM152873 1 0.0771 0.7960 0.976 0.000 0.004 0.020 0.000
#> GSM152874 1 0.1168 0.7943 0.960 0.000 0.008 0.032 0.000
#> GSM152875 1 0.0798 0.7956 0.976 0.000 0.008 0.016 0.000
#> GSM152876 1 0.1915 0.7620 0.928 0.000 0.032 0.040 0.000
#> GSM152877 1 0.1041 0.7947 0.964 0.000 0.004 0.032 0.000
#> GSM152878 1 0.0162 0.7935 0.996 0.000 0.004 0.000 0.000
#> GSM152879 1 0.0404 0.7935 0.988 0.000 0.000 0.012 0.000
#> GSM152880 1 0.1251 0.7931 0.956 0.000 0.008 0.036 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.5876 0.61154 0.024 0.684 0.060 0.072 0.144 0.016
#> GSM152805 5 0.1836 0.77249 0.000 0.004 0.048 0.008 0.928 0.012
#> GSM152806 5 0.0935 0.77807 0.000 0.000 0.032 0.004 0.964 0.000
#> GSM152807 2 0.1606 0.79778 0.000 0.932 0.004 0.056 0.000 0.008
#> GSM152808 5 0.0891 0.77772 0.000 0.000 0.024 0.000 0.968 0.008
#> GSM152809 2 0.1204 0.79925 0.000 0.944 0.000 0.056 0.000 0.000
#> GSM152810 6 0.5590 0.21911 0.008 0.000 0.004 0.100 0.376 0.512
#> GSM152811 5 0.1679 0.77599 0.000 0.000 0.036 0.012 0.936 0.016
#> GSM152812 2 0.0653 0.81014 0.004 0.980 0.000 0.012 0.000 0.004
#> GSM152813 2 0.1794 0.80733 0.000 0.932 0.028 0.024 0.000 0.016
#> GSM152814 2 0.2325 0.80380 0.008 0.916 0.020 0.016 0.028 0.012
#> GSM152815 2 0.0862 0.81086 0.004 0.972 0.000 0.016 0.000 0.008
#> GSM152816 5 0.5009 0.63950 0.000 0.144 0.112 0.012 0.712 0.020
#> GSM152817 5 0.1088 0.77689 0.000 0.000 0.024 0.000 0.960 0.016
#> GSM152818 5 0.0937 0.77683 0.000 0.000 0.040 0.000 0.960 0.000
#> GSM152819 5 0.3620 0.62068 0.004 0.228 0.000 0.004 0.752 0.012
#> GSM152820 5 0.5208 0.47580 0.000 0.316 0.024 0.024 0.612 0.024
#> GSM152821 2 0.2468 0.77919 0.000 0.884 0.004 0.008 0.092 0.012
#> GSM153115 4 0.6870 0.40294 0.120 0.088 0.292 0.488 0.000 0.012
#> GSM153116 5 0.2144 0.75718 0.000 0.048 0.004 0.004 0.912 0.032
#> GSM153117 5 0.2573 0.71749 0.000 0.132 0.008 0.000 0.856 0.004
#> GSM153118 2 0.2492 0.78965 0.000 0.888 0.008 0.004 0.080 0.020
#> GSM153119 5 0.3936 0.51258 0.000 0.004 0.020 0.000 0.700 0.276
#> GSM153120 6 0.7356 -0.04130 0.056 0.272 0.004 0.292 0.012 0.364
#> GSM153121 3 0.2917 0.74959 0.000 0.028 0.868 0.000 0.072 0.032
#> GSM153122 6 0.6062 0.15218 0.000 0.000 0.212 0.008 0.312 0.468
#> GSM153123 2 0.5596 0.27159 0.000 0.524 0.376 0.020 0.004 0.076
#> GSM153124 3 0.5371 0.06035 0.000 0.088 0.512 0.392 0.000 0.008
#> GSM153125 4 0.5998 0.50868 0.048 0.312 0.088 0.548 0.000 0.004
#> GSM153126 3 0.2182 0.74529 0.000 0.000 0.900 0.004 0.076 0.020
#> GSM153127 2 0.1088 0.81022 0.000 0.960 0.000 0.024 0.000 0.016
#> GSM153128 6 0.5413 0.43707 0.000 0.068 0.100 0.044 0.068 0.720
#> GSM153129 3 0.3912 0.72594 0.000 0.108 0.808 0.024 0.048 0.012
#> GSM153130 3 0.3950 0.60877 0.000 0.004 0.708 0.004 0.268 0.016
#> GSM153131 3 0.5943 0.25990 0.000 0.100 0.488 0.008 0.384 0.020
#> GSM153132 5 0.5517 0.37067 0.000 0.356 0.072 0.000 0.544 0.028
#> GSM153133 2 0.4186 0.72066 0.000 0.772 0.132 0.028 0.000 0.068
#> GSM153134 3 0.6060 0.31176 0.000 0.372 0.484 0.008 0.116 0.020
#> GSM153135 2 0.0993 0.80954 0.000 0.964 0.000 0.024 0.000 0.012
#> GSM153136 4 0.6352 0.50988 0.084 0.312 0.072 0.524 0.000 0.008
#> GSM153137 2 0.2776 0.77171 0.000 0.860 0.000 0.052 0.000 0.088
#> GSM153138 2 0.3976 0.70737 0.000 0.776 0.008 0.088 0.000 0.128
#> GSM153139 3 0.5266 0.43819 0.000 0.052 0.576 0.008 0.348 0.016
#> GSM153140 2 0.4970 0.48934 0.008 0.668 0.064 0.248 0.004 0.008
#> GSM153141 2 0.0914 0.80989 0.000 0.968 0.000 0.016 0.000 0.016
#> GSM153142 5 0.1341 0.77729 0.000 0.000 0.028 0.000 0.948 0.024
#> GSM153143 2 0.3632 0.67022 0.004 0.800 0.008 0.148 0.000 0.040
#> GSM153144 2 0.3809 0.66190 0.000 0.756 0.208 0.020 0.000 0.016
#> GSM153145 5 0.1257 0.77657 0.000 0.000 0.028 0.000 0.952 0.020
#> GSM153146 2 0.1549 0.81101 0.000 0.944 0.004 0.004 0.024 0.024
#> GSM153147 3 0.3007 0.73383 0.000 0.080 0.860 0.000 0.020 0.040
#> GSM153148 2 0.0520 0.81046 0.000 0.984 0.000 0.008 0.000 0.008
#> GSM153149 2 0.2222 0.80443 0.000 0.908 0.040 0.000 0.012 0.040
#> GSM153150 4 0.6463 0.18972 0.004 0.216 0.012 0.428 0.004 0.336
#> GSM153151 6 0.6942 0.27550 0.000 0.240 0.232 0.040 0.020 0.468
#> GSM153152 2 0.5681 0.32796 0.000 0.560 0.340 0.012 0.036 0.052
#> GSM153153 2 0.3284 0.75363 0.004 0.840 0.012 0.008 0.116 0.020
#> GSM153154 5 0.5004 0.59027 0.000 0.092 0.196 0.004 0.688 0.020
#> GSM153155 2 0.1426 0.81229 0.000 0.948 0.028 0.008 0.000 0.016
#> GSM153156 3 0.3626 0.74541 0.000 0.036 0.828 0.008 0.096 0.032
#> GSM153157 5 0.2426 0.76399 0.000 0.000 0.044 0.012 0.896 0.048
#> GSM153158 5 0.1562 0.77896 0.000 0.024 0.032 0.000 0.940 0.004
#> GSM153159 5 0.2209 0.76801 0.000 0.000 0.052 0.004 0.904 0.040
#> GSM153160 3 0.1738 0.74278 0.000 0.000 0.928 0.004 0.052 0.016
#> GSM153161 2 0.2070 0.79204 0.000 0.908 0.000 0.044 0.000 0.048
#> GSM153162 3 0.2533 0.75566 0.000 0.044 0.892 0.004 0.052 0.008
#> GSM153163 5 0.4901 0.07758 0.000 0.020 0.424 0.004 0.532 0.020
#> GSM153164 5 0.2827 0.70376 0.000 0.132 0.004 0.008 0.848 0.008
#> GSM153165 3 0.3976 0.72177 0.004 0.024 0.784 0.008 0.160 0.020
#> GSM153166 2 0.4885 0.64187 0.000 0.716 0.080 0.012 0.172 0.020
#> GSM153167 3 0.4734 0.58558 0.000 0.240 0.692 0.036 0.012 0.020
#> GSM153168 5 0.1565 0.77432 0.000 0.000 0.028 0.004 0.940 0.028
#> GSM153169 3 0.4055 0.67390 0.000 0.016 0.744 0.004 0.212 0.024
#> GSM153170 3 0.2999 0.74961 0.000 0.048 0.840 0.000 0.112 0.000
#> GSM153171 4 0.6511 0.37284 0.068 0.056 0.316 0.524 0.000 0.036
#> GSM153172 2 0.1605 0.81178 0.000 0.940 0.032 0.016 0.000 0.012
#> GSM153173 3 0.3589 0.69965 0.004 0.008 0.776 0.000 0.196 0.016
#> GSM153174 3 0.2846 0.71790 0.000 0.116 0.856 0.016 0.004 0.008
#> GSM153175 3 0.3596 0.55891 0.016 0.000 0.760 0.216 0.000 0.008
#> GSM153176 3 0.2907 0.70621 0.004 0.000 0.868 0.084 0.020 0.024
#> GSM153177 2 0.3201 0.77867 0.000 0.852 0.044 0.000 0.072 0.032
#> GSM152931 4 0.6581 0.49857 0.048 0.288 0.172 0.488 0.000 0.004
#> GSM152932 2 0.2351 0.80336 0.000 0.900 0.052 0.012 0.000 0.036
#> GSM152933 2 0.4213 0.52509 0.000 0.684 0.008 0.000 0.280 0.028
#> GSM152934 6 0.6525 0.27975 0.000 0.116 0.084 0.224 0.012 0.564
#> GSM152935 6 0.7185 0.16062 0.000 0.136 0.040 0.052 0.364 0.408
#> GSM152936 4 0.6628 0.40055 0.000 0.344 0.072 0.448 0.000 0.136
#> GSM152937 6 0.4842 0.29046 0.000 0.020 0.308 0.008 0.028 0.636
#> GSM152938 3 0.3444 0.68411 0.000 0.012 0.812 0.000 0.036 0.140
#> GSM152939 3 0.3907 0.59641 0.020 0.016 0.776 0.176 0.000 0.012
#> GSM152940 6 0.5866 -0.10579 0.000 0.136 0.012 0.412 0.000 0.440
#> GSM152941 4 0.5659 -0.00667 0.104 0.004 0.004 0.548 0.008 0.332
#> GSM152942 3 0.1708 0.73992 0.000 0.000 0.932 0.024 0.040 0.004
#> GSM152943 6 0.6047 0.25811 0.000 0.176 0.036 0.200 0.004 0.584
#> GSM152944 5 0.4397 0.41244 0.000 0.024 0.316 0.000 0.648 0.012
#> GSM152945 6 0.6204 0.36667 0.008 0.080 0.020 0.156 0.092 0.644
#> GSM152946 2 0.6636 0.34935 0.000 0.536 0.200 0.180 0.004 0.080
#> GSM152947 4 0.6459 0.04172 0.028 0.020 0.088 0.428 0.008 0.428
#> GSM152948 2 0.1251 0.81099 0.000 0.956 0.012 0.024 0.000 0.008
#> GSM152949 3 0.3129 0.75364 0.000 0.056 0.852 0.004 0.080 0.008
#> GSM152950 3 0.6771 0.39687 0.000 0.276 0.476 0.000 0.164 0.084
#> GSM152951 2 0.1767 0.80721 0.000 0.932 0.020 0.036 0.000 0.012
#> GSM152952 2 0.1789 0.79748 0.000 0.924 0.000 0.044 0.000 0.032
#> GSM152953 2 0.1605 0.81135 0.000 0.936 0.004 0.016 0.000 0.044
#> GSM152954 4 0.4832 0.49279 0.040 0.164 0.024 0.740 0.008 0.024
#> GSM152955 5 0.5479 0.27931 0.000 0.016 0.000 0.116 0.592 0.276
#> GSM152956 2 0.0914 0.81046 0.000 0.968 0.000 0.016 0.000 0.016
#> GSM152957 3 0.5178 0.29813 0.032 0.004 0.576 0.356 0.000 0.032
#> GSM152958 4 0.5093 0.51990 0.036 0.296 0.024 0.632 0.000 0.012
#> GSM152959 4 0.4469 0.28963 0.004 0.008 0.084 0.744 0.004 0.156
#> GSM152960 2 0.6046 -0.09398 0.004 0.468 0.008 0.352 0.000 0.168
#> GSM152961 4 0.5319 0.49878 0.132 0.164 0.028 0.672 0.004 0.000
#> GSM152962 6 0.7158 0.23632 0.000 0.184 0.260 0.024 0.064 0.468
#> GSM152963 2 0.1225 0.80716 0.000 0.952 0.000 0.012 0.000 0.036
#> GSM152964 6 0.4928 0.17469 0.000 0.008 0.004 0.040 0.392 0.556
#> GSM152965 2 0.4006 0.67061 0.000 0.756 0.008 0.040 0.004 0.192
#> GSM152966 4 0.6473 0.51770 0.068 0.292 0.108 0.524 0.000 0.008
#> GSM152967 2 0.2318 0.80659 0.000 0.904 0.028 0.048 0.000 0.020
#> GSM152968 3 0.5570 0.60141 0.000 0.184 0.632 0.000 0.152 0.032
#> GSM152969 4 0.4881 0.51431 0.008 0.308 0.032 0.636 0.004 0.012
#> GSM152970 4 0.6636 0.06179 0.052 0.008 0.148 0.484 0.000 0.308
#> GSM152971 4 0.5678 0.42654 0.024 0.376 0.068 0.524 0.000 0.008
#> GSM152972 4 0.5208 0.31877 0.012 0.436 0.036 0.504 0.000 0.012
#> GSM152973 3 0.2015 0.71452 0.016 0.000 0.916 0.056 0.000 0.012
#> GSM152974 2 0.1718 0.81124 0.000 0.932 0.044 0.008 0.000 0.016
#> GSM152975 2 0.6024 0.00929 0.000 0.412 0.000 0.204 0.380 0.004
#> GSM152976 4 0.5753 0.23175 0.124 0.000 0.380 0.484 0.000 0.012
#> GSM152977 4 0.4960 0.21298 0.020 0.000 0.012 0.716 0.148 0.104
#> GSM152978 4 0.5049 0.44283 0.008 0.352 0.000 0.584 0.008 0.048
#> GSM152979 3 0.3250 0.72017 0.000 0.004 0.808 0.004 0.168 0.016
#> GSM152980 2 0.5035 0.37734 0.000 0.612 0.020 0.324 0.008 0.036
#> GSM152981 5 0.2851 0.70622 0.000 0.000 0.020 0.004 0.844 0.132
#> GSM152982 3 0.5523 0.13369 0.000 0.008 0.516 0.392 0.012 0.072
#> GSM152983 4 0.5455 0.50750 0.016 0.164 0.116 0.676 0.000 0.028
#> GSM152984 3 0.1858 0.72270 0.000 0.000 0.924 0.052 0.012 0.012
#> GSM152985 4 0.3841 0.23967 0.012 0.004 0.004 0.748 0.008 0.224
#> GSM152986 4 0.6187 0.52587 0.084 0.292 0.072 0.548 0.000 0.004
#> GSM152987 6 0.4225 0.38107 0.076 0.004 0.004 0.152 0.004 0.760
#> GSM152988 3 0.3123 0.66936 0.032 0.000 0.840 0.116 0.000 0.012
#> GSM152989 4 0.4667 0.30518 0.160 0.000 0.048 0.732 0.000 0.060
#> GSM152990 3 0.2545 0.75256 0.000 0.020 0.884 0.004 0.084 0.008
#> GSM152991 5 0.4917 0.51878 0.000 0.228 0.000 0.004 0.656 0.112
#> GSM187524 6 0.5405 0.34190 0.100 0.000 0.004 0.248 0.020 0.628
#> GSM187525 6 0.5899 0.25057 0.116 0.000 0.004 0.380 0.016 0.484
#> GSM187526 4 0.6674 -0.25431 0.320 0.000 0.008 0.368 0.016 0.288
#> GSM187527 1 0.1911 0.84338 0.928 0.000 0.012 0.036 0.004 0.020
#> GSM152856 1 0.0520 0.84909 0.984 0.000 0.000 0.008 0.000 0.008
#> GSM152857 1 0.2068 0.79755 0.904 0.000 0.008 0.000 0.080 0.008
#> GSM152858 4 0.6543 -0.30925 0.316 0.000 0.008 0.356 0.008 0.312
#> GSM152859 6 0.5765 0.29033 0.128 0.000 0.004 0.288 0.016 0.564
#> GSM152860 6 0.6342 0.05630 0.236 0.000 0.004 0.360 0.008 0.392
#> GSM152861 1 0.5567 0.58808 0.592 0.000 0.008 0.252 0.004 0.144
#> GSM152862 6 0.6346 0.05878 0.236 0.000 0.004 0.372 0.008 0.380
#> GSM152863 1 0.4136 0.79689 0.780 0.000 0.016 0.112 0.004 0.088
#> GSM152864 1 0.3315 0.82118 0.836 0.000 0.012 0.108 0.004 0.040
#> GSM152865 1 0.4993 0.68245 0.664 0.000 0.008 0.228 0.004 0.096
#> GSM152866 1 0.4363 0.73841 0.744 0.000 0.008 0.056 0.012 0.180
#> GSM152867 1 0.2136 0.84091 0.908 0.000 0.012 0.064 0.000 0.016
#> GSM152868 1 0.3756 0.79731 0.792 0.000 0.016 0.156 0.004 0.032
#> GSM152869 1 0.3592 0.79954 0.800 0.000 0.012 0.156 0.004 0.028
#> GSM152870 6 0.6295 0.09214 0.220 0.000 0.004 0.364 0.008 0.404
#> GSM152871 1 0.6377 0.28804 0.416 0.000 0.008 0.348 0.008 0.220
#> GSM152872 4 0.6518 -0.27462 0.292 0.000 0.008 0.380 0.008 0.312
#> GSM152873 1 0.1296 0.84683 0.948 0.000 0.000 0.004 0.004 0.044
#> GSM152874 1 0.1912 0.84584 0.924 0.000 0.008 0.008 0.008 0.052
#> GSM152875 1 0.1711 0.84481 0.936 0.000 0.008 0.008 0.008 0.040
#> GSM152876 1 0.1596 0.82500 0.944 0.000 0.012 0.020 0.004 0.020
#> GSM152877 1 0.1757 0.84588 0.928 0.000 0.000 0.012 0.008 0.052
#> GSM152878 1 0.1691 0.83982 0.940 0.000 0.012 0.012 0.008 0.028
#> GSM152879 1 0.0363 0.84811 0.988 0.000 0.000 0.012 0.000 0.000
#> GSM152880 1 0.1124 0.84980 0.956 0.000 0.000 0.008 0.000 0.036
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> SD:NMF 166 2.46e-15 2
#> SD:NMF 154 1.89e-17 3
#> SD:NMF 120 2.41e-15 4
#> SD:NMF 118 4.30e-23 5
#> SD:NMF 110 2.61e-21 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "hclust"]
# you can also extract it by
# res = res_list["CV:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.730 0.922 0.945 0.3328 0.701 0.701
#> 3 3 0.413 0.649 0.864 0.3228 0.990 0.986
#> 4 4 0.400 0.672 0.812 0.1776 0.877 0.823
#> 5 5 0.404 0.677 0.750 0.0780 0.972 0.951
#> 6 6 0.396 0.673 0.713 0.0758 0.985 0.972
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.2043 0.941 0.032 0.968
#> GSM152805 2 0.0672 0.940 0.008 0.992
#> GSM152806 2 0.0672 0.940 0.008 0.992
#> GSM152807 2 0.2423 0.939 0.040 0.960
#> GSM152808 2 0.0672 0.940 0.008 0.992
#> GSM152809 2 0.2423 0.939 0.040 0.960
#> GSM152810 2 0.7219 0.774 0.200 0.800
#> GSM152811 2 0.2778 0.928 0.048 0.952
#> GSM152812 2 0.2423 0.939 0.040 0.960
#> GSM152813 2 0.1414 0.943 0.020 0.980
#> GSM152814 2 0.1633 0.943 0.024 0.976
#> GSM152815 2 0.2423 0.939 0.040 0.960
#> GSM152816 2 0.0672 0.942 0.008 0.992
#> GSM152817 2 0.0672 0.940 0.008 0.992
#> GSM152818 2 0.0672 0.940 0.008 0.992
#> GSM152819 2 0.0376 0.941 0.004 0.996
#> GSM152820 2 0.3431 0.931 0.064 0.936
#> GSM152821 2 0.1843 0.942 0.028 0.972
#> GSM153115 2 0.6973 0.837 0.188 0.812
#> GSM153116 2 0.0672 0.940 0.008 0.992
#> GSM153117 2 0.0000 0.942 0.000 1.000
#> GSM153118 2 0.2043 0.941 0.032 0.968
#> GSM153119 2 0.0672 0.940 0.008 0.992
#> GSM153120 2 0.7139 0.834 0.196 0.804
#> GSM153121 2 0.0672 0.940 0.008 0.992
#> GSM153122 2 0.0672 0.940 0.008 0.992
#> GSM153123 2 0.0672 0.940 0.008 0.992
#> GSM153124 2 0.5178 0.897 0.116 0.884
#> GSM153125 2 0.6712 0.849 0.176 0.824
#> GSM153126 2 0.0672 0.940 0.008 0.992
#> GSM153127 2 0.2423 0.939 0.040 0.960
#> GSM153128 2 0.0672 0.942 0.008 0.992
#> GSM153129 2 0.0938 0.943 0.012 0.988
#> GSM153130 2 0.0672 0.940 0.008 0.992
#> GSM153131 2 0.0000 0.942 0.000 1.000
#> GSM153132 2 0.0376 0.942 0.004 0.996
#> GSM153133 2 0.0938 0.943 0.012 0.988
#> GSM153134 2 0.0672 0.943 0.008 0.992
#> GSM153135 2 0.2236 0.939 0.036 0.964
#> GSM153136 2 0.7219 0.825 0.200 0.800
#> GSM153137 2 0.3274 0.931 0.060 0.940
#> GSM153138 2 0.1843 0.942 0.028 0.972
#> GSM153139 2 0.0672 0.940 0.008 0.992
#> GSM153140 2 0.2043 0.942 0.032 0.968
#> GSM153141 2 0.2603 0.937 0.044 0.956
#> GSM153142 2 0.0672 0.940 0.008 0.992
#> GSM153143 2 0.2603 0.938 0.044 0.956
#> GSM153144 2 0.1184 0.943 0.016 0.984
#> GSM153145 2 0.0672 0.940 0.008 0.992
#> GSM153146 2 0.2043 0.941 0.032 0.968
#> GSM153147 2 0.0672 0.940 0.008 0.992
#> GSM153148 2 0.2423 0.939 0.040 0.960
#> GSM153149 2 0.1843 0.942 0.028 0.972
#> GSM153150 2 0.7219 0.828 0.200 0.800
#> GSM153151 2 0.0672 0.940 0.008 0.992
#> GSM153152 2 0.0376 0.942 0.004 0.996
#> GSM153153 2 0.0938 0.943 0.012 0.988
#> GSM153154 2 0.0376 0.942 0.004 0.996
#> GSM153155 2 0.1414 0.943 0.020 0.980
#> GSM153156 2 0.0672 0.940 0.008 0.992
#> GSM153157 2 0.0672 0.940 0.008 0.992
#> GSM153158 2 0.0000 0.942 0.000 1.000
#> GSM153159 2 0.0672 0.940 0.008 0.992
#> GSM153160 2 0.0672 0.940 0.008 0.992
#> GSM153161 2 0.2423 0.938 0.040 0.960
#> GSM153162 2 0.0672 0.943 0.008 0.992
#> GSM153163 2 0.0672 0.940 0.008 0.992
#> GSM153164 2 0.2603 0.937 0.044 0.956
#> GSM153165 2 0.0672 0.940 0.008 0.992
#> GSM153166 2 0.1414 0.943 0.020 0.980
#> GSM153167 2 0.0672 0.943 0.008 0.992
#> GSM153168 2 0.0672 0.940 0.008 0.992
#> GSM153169 2 0.0938 0.941 0.012 0.988
#> GSM153170 2 0.0672 0.940 0.008 0.992
#> GSM153171 2 0.6623 0.855 0.172 0.828
#> GSM153172 2 0.1414 0.943 0.020 0.980
#> GSM153173 2 0.0672 0.940 0.008 0.992
#> GSM153174 2 0.0672 0.943 0.008 0.992
#> GSM153175 2 0.6148 0.868 0.152 0.848
#> GSM153176 2 0.5842 0.878 0.140 0.860
#> GSM153177 2 0.1184 0.943 0.016 0.984
#> GSM152931 2 0.6801 0.846 0.180 0.820
#> GSM152932 2 0.1184 0.943 0.016 0.984
#> GSM152933 2 0.1633 0.942 0.024 0.976
#> GSM152934 2 0.4431 0.913 0.092 0.908
#> GSM152935 2 0.0376 0.941 0.004 0.996
#> GSM152936 2 0.6623 0.856 0.172 0.828
#> GSM152937 2 0.0672 0.940 0.008 0.992
#> GSM152938 2 0.0672 0.940 0.008 0.992
#> GSM152939 2 0.1184 0.942 0.016 0.984
#> GSM152940 2 0.8016 0.774 0.244 0.756
#> GSM152941 1 0.3879 0.919 0.924 0.076
#> GSM152942 2 0.0938 0.944 0.012 0.988
#> GSM152943 2 0.2236 0.940 0.036 0.964
#> GSM152944 2 0.0376 0.941 0.004 0.996
#> GSM152945 2 0.1633 0.939 0.024 0.976
#> GSM152946 2 0.4022 0.918 0.080 0.920
#> GSM152947 2 0.7602 0.804 0.220 0.780
#> GSM152948 2 0.2236 0.940 0.036 0.964
#> GSM152949 2 0.0376 0.942 0.004 0.996
#> GSM152950 2 0.0376 0.942 0.004 0.996
#> GSM152951 2 0.2236 0.941 0.036 0.964
#> GSM152952 2 0.2423 0.939 0.040 0.960
#> GSM152953 2 0.2236 0.940 0.036 0.964
#> GSM152954 2 0.7376 0.818 0.208 0.792
#> GSM152955 2 0.0938 0.943 0.012 0.988
#> GSM152956 2 0.2423 0.939 0.040 0.960
#> GSM152957 2 0.7139 0.829 0.196 0.804
#> GSM152958 2 0.7299 0.820 0.204 0.796
#> GSM152959 2 0.7376 0.818 0.208 0.792
#> GSM152960 2 0.7453 0.813 0.212 0.788
#> GSM152961 2 0.7815 0.790 0.232 0.768
#> GSM152962 2 0.0672 0.940 0.008 0.992
#> GSM152963 2 0.2603 0.937 0.044 0.956
#> GSM152964 2 0.0672 0.940 0.008 0.992
#> GSM152965 2 0.0672 0.943 0.008 0.992
#> GSM152966 2 0.6801 0.845 0.180 0.820
#> GSM152967 2 0.0672 0.943 0.008 0.992
#> GSM152968 2 0.0376 0.942 0.004 0.996
#> GSM152969 2 0.6887 0.841 0.184 0.816
#> GSM152970 2 0.7745 0.794 0.228 0.772
#> GSM152971 2 0.6887 0.841 0.184 0.816
#> GSM152972 2 0.7299 0.820 0.204 0.796
#> GSM152973 2 0.0938 0.941 0.012 0.988
#> GSM152974 2 0.1843 0.942 0.028 0.972
#> GSM152975 2 0.3431 0.927 0.064 0.936
#> GSM152976 2 0.6438 0.859 0.164 0.836
#> GSM152977 2 0.6048 0.872 0.148 0.852
#> GSM152978 2 0.6712 0.852 0.176 0.824
#> GSM152979 2 0.0672 0.940 0.008 0.992
#> GSM152980 2 0.3584 0.928 0.068 0.932
#> GSM152981 2 0.0672 0.940 0.008 0.992
#> GSM152982 2 0.6048 0.872 0.148 0.852
#> GSM152983 2 0.6973 0.838 0.188 0.812
#> GSM152984 2 0.0672 0.940 0.008 0.992
#> GSM152985 2 0.7528 0.808 0.216 0.784
#> GSM152986 2 0.7219 0.824 0.200 0.800
#> GSM152987 1 0.9833 0.219 0.576 0.424
#> GSM152988 2 0.2043 0.940 0.032 0.968
#> GSM152989 2 0.7219 0.825 0.200 0.800
#> GSM152990 2 0.0376 0.941 0.004 0.996
#> GSM152991 2 0.0938 0.943 0.012 0.988
#> GSM187524 1 0.1414 0.981 0.980 0.020
#> GSM187525 1 0.1414 0.981 0.980 0.020
#> GSM187526 1 0.1414 0.981 0.980 0.020
#> GSM187527 1 0.1414 0.981 0.980 0.020
#> GSM152856 1 0.1184 0.980 0.984 0.016
#> GSM152857 1 0.1184 0.980 0.984 0.016
#> GSM152858 1 0.1414 0.981 0.980 0.020
#> GSM152859 1 0.2236 0.968 0.964 0.036
#> GSM152860 1 0.1414 0.981 0.980 0.020
#> GSM152861 1 0.1414 0.981 0.980 0.020
#> GSM152862 1 0.1414 0.981 0.980 0.020
#> GSM152863 1 0.1414 0.981 0.980 0.020
#> GSM152864 1 0.1414 0.981 0.980 0.020
#> GSM152865 1 0.1414 0.981 0.980 0.020
#> GSM152866 1 0.1184 0.980 0.984 0.016
#> GSM152867 1 0.1414 0.981 0.980 0.020
#> GSM152868 1 0.1414 0.981 0.980 0.020
#> GSM152869 1 0.1414 0.981 0.980 0.020
#> GSM152870 1 0.1414 0.981 0.980 0.020
#> GSM152871 1 0.1414 0.981 0.980 0.020
#> GSM152872 1 0.1414 0.981 0.980 0.020
#> GSM152873 1 0.1184 0.980 0.984 0.016
#> GSM152874 1 0.1184 0.980 0.984 0.016
#> GSM152875 1 0.1184 0.980 0.984 0.016
#> GSM152876 1 0.1184 0.980 0.984 0.016
#> GSM152877 1 0.1184 0.980 0.984 0.016
#> GSM152878 1 0.1184 0.980 0.984 0.016
#> GSM152879 1 0.1184 0.980 0.984 0.016
#> GSM152880 1 0.1184 0.980 0.984 0.016
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.2955 0.717 0.008 0.912 0.080
#> GSM152805 2 0.5733 0.129 0.000 0.676 0.324
#> GSM152806 2 0.5733 0.129 0.000 0.676 0.324
#> GSM152807 2 0.3359 0.712 0.016 0.900 0.084
#> GSM152808 2 0.5733 0.129 0.000 0.676 0.324
#> GSM152809 2 0.3359 0.712 0.016 0.900 0.084
#> GSM152810 2 0.7378 -0.270 0.052 0.628 0.320
#> GSM152811 2 0.5493 0.382 0.012 0.756 0.232
#> GSM152812 2 0.3359 0.712 0.016 0.900 0.084
#> GSM152813 2 0.2384 0.729 0.008 0.936 0.056
#> GSM152814 2 0.2651 0.727 0.012 0.928 0.060
#> GSM152815 2 0.3445 0.710 0.016 0.896 0.088
#> GSM152816 2 0.2356 0.700 0.000 0.928 0.072
#> GSM152817 2 0.5733 0.129 0.000 0.676 0.324
#> GSM152818 2 0.5733 0.129 0.000 0.676 0.324
#> GSM152819 2 0.3038 0.666 0.000 0.896 0.104
#> GSM152820 2 0.3910 0.696 0.020 0.876 0.104
#> GSM152821 2 0.2229 0.728 0.012 0.944 0.044
#> GSM153115 2 0.7138 0.486 0.120 0.720 0.160
#> GSM153116 2 0.5529 0.228 0.000 0.704 0.296
#> GSM153117 2 0.3619 0.619 0.000 0.864 0.136
#> GSM153118 2 0.2446 0.728 0.012 0.936 0.052
#> GSM153119 2 0.4654 0.501 0.000 0.792 0.208
#> GSM153120 2 0.7542 0.425 0.120 0.688 0.192
#> GSM153121 2 0.3192 0.657 0.000 0.888 0.112
#> GSM153122 2 0.5254 0.348 0.000 0.736 0.264
#> GSM153123 2 0.2959 0.692 0.000 0.900 0.100
#> GSM153124 2 0.5449 0.629 0.068 0.816 0.116
#> GSM153125 2 0.6892 0.510 0.112 0.736 0.152
#> GSM153126 2 0.3116 0.660 0.000 0.892 0.108
#> GSM153127 2 0.3528 0.707 0.016 0.892 0.092
#> GSM153128 2 0.3193 0.680 0.004 0.896 0.100
#> GSM153129 2 0.1765 0.727 0.004 0.956 0.040
#> GSM153130 2 0.3038 0.661 0.000 0.896 0.104
#> GSM153131 2 0.1643 0.715 0.000 0.956 0.044
#> GSM153132 2 0.0747 0.721 0.000 0.984 0.016
#> GSM153133 2 0.1585 0.728 0.008 0.964 0.028
#> GSM153134 2 0.1163 0.721 0.000 0.972 0.028
#> GSM153135 2 0.3293 0.712 0.012 0.900 0.088
#> GSM153136 2 0.7319 0.459 0.128 0.708 0.164
#> GSM153137 2 0.4094 0.699 0.028 0.872 0.100
#> GSM153138 2 0.2955 0.719 0.008 0.912 0.080
#> GSM153139 2 0.3038 0.661 0.000 0.896 0.104
#> GSM153140 2 0.3141 0.722 0.020 0.912 0.068
#> GSM153141 2 0.3610 0.705 0.016 0.888 0.096
#> GSM153142 2 0.5529 0.228 0.000 0.704 0.296
#> GSM153143 2 0.3461 0.714 0.024 0.900 0.076
#> GSM153144 2 0.2173 0.721 0.008 0.944 0.048
#> GSM153145 2 0.5733 0.129 0.000 0.676 0.324
#> GSM153146 2 0.2339 0.729 0.012 0.940 0.048
#> GSM153147 2 0.2537 0.690 0.000 0.920 0.080
#> GSM153148 2 0.3528 0.707 0.016 0.892 0.092
#> GSM153149 2 0.2866 0.723 0.008 0.916 0.076
#> GSM153150 2 0.7309 0.468 0.124 0.708 0.168
#> GSM153151 2 0.2448 0.700 0.000 0.924 0.076
#> GSM153152 2 0.1289 0.724 0.000 0.968 0.032
#> GSM153153 2 0.1315 0.728 0.008 0.972 0.020
#> GSM153154 2 0.1964 0.713 0.000 0.944 0.056
#> GSM153155 2 0.2116 0.729 0.012 0.948 0.040
#> GSM153156 2 0.3192 0.657 0.000 0.888 0.112
#> GSM153157 2 0.3686 0.613 0.000 0.860 0.140
#> GSM153158 2 0.4654 0.455 0.000 0.792 0.208
#> GSM153159 2 0.5465 0.258 0.000 0.712 0.288
#> GSM153160 2 0.3412 0.642 0.000 0.876 0.124
#> GSM153161 2 0.3539 0.708 0.012 0.888 0.100
#> GSM153162 2 0.1878 0.717 0.004 0.952 0.044
#> GSM153163 2 0.2625 0.682 0.000 0.916 0.084
#> GSM153164 2 0.4575 0.645 0.012 0.828 0.160
#> GSM153165 2 0.2537 0.686 0.000 0.920 0.080
#> GSM153166 2 0.2173 0.728 0.008 0.944 0.048
#> GSM153167 2 0.1163 0.721 0.000 0.972 0.028
#> GSM153168 2 0.5760 0.115 0.000 0.672 0.328
#> GSM153169 2 0.2625 0.686 0.000 0.916 0.084
#> GSM153170 2 0.2356 0.693 0.000 0.928 0.072
#> GSM153171 2 0.6530 0.548 0.120 0.760 0.120
#> GSM153172 2 0.2339 0.728 0.012 0.940 0.048
#> GSM153173 2 0.2537 0.686 0.000 0.920 0.080
#> GSM153174 2 0.1878 0.717 0.004 0.952 0.044
#> GSM153175 2 0.6332 0.558 0.088 0.768 0.144
#> GSM153176 2 0.6171 0.572 0.080 0.776 0.144
#> GSM153177 2 0.1711 0.727 0.008 0.960 0.032
#> GSM152931 2 0.7004 0.503 0.112 0.728 0.160
#> GSM152932 2 0.2096 0.731 0.004 0.944 0.052
#> GSM152933 2 0.2116 0.728 0.012 0.948 0.040
#> GSM152934 2 0.4995 0.678 0.068 0.840 0.092
#> GSM152935 2 0.3340 0.667 0.000 0.880 0.120
#> GSM152936 2 0.6519 0.551 0.108 0.760 0.132
#> GSM152937 2 0.2796 0.680 0.000 0.908 0.092
#> GSM152938 2 0.2796 0.680 0.000 0.908 0.092
#> GSM152939 2 0.2955 0.711 0.008 0.912 0.080
#> GSM152940 2 0.8162 0.304 0.164 0.644 0.192
#> GSM152941 1 0.4339 0.858 0.868 0.048 0.084
#> GSM152942 2 0.2486 0.717 0.008 0.932 0.060
#> GSM152943 2 0.3618 0.714 0.012 0.884 0.104
#> GSM152944 2 0.2261 0.699 0.000 0.932 0.068
#> GSM152945 3 0.6215 0.000 0.000 0.428 0.572
#> GSM152946 2 0.4742 0.676 0.048 0.848 0.104
#> GSM152947 2 0.7562 0.417 0.148 0.692 0.160
#> GSM152948 2 0.3120 0.719 0.012 0.908 0.080
#> GSM152949 2 0.1643 0.718 0.000 0.956 0.044
#> GSM152950 2 0.0892 0.726 0.000 0.980 0.020
#> GSM152951 2 0.2998 0.724 0.016 0.916 0.068
#> GSM152952 2 0.3445 0.709 0.016 0.896 0.088
#> GSM152953 2 0.3043 0.716 0.008 0.908 0.084
#> GSM152954 2 0.7424 0.449 0.128 0.700 0.172
#> GSM152955 2 0.3686 0.662 0.000 0.860 0.140
#> GSM152956 2 0.3528 0.707 0.016 0.892 0.092
#> GSM152957 2 0.7202 0.472 0.124 0.716 0.160
#> GSM152958 2 0.7381 0.451 0.132 0.704 0.164
#> GSM152959 2 0.7424 0.448 0.128 0.700 0.172
#> GSM152960 2 0.7424 0.447 0.128 0.700 0.172
#> GSM152961 2 0.7772 0.392 0.152 0.676 0.172
#> GSM152962 2 0.2796 0.691 0.000 0.908 0.092
#> GSM152963 2 0.3610 0.705 0.016 0.888 0.096
#> GSM152964 2 0.5591 0.207 0.000 0.696 0.304
#> GSM152965 2 0.1950 0.730 0.008 0.952 0.040
#> GSM152966 2 0.7004 0.501 0.112 0.728 0.160
#> GSM152967 2 0.1765 0.727 0.004 0.956 0.040
#> GSM152968 2 0.1860 0.716 0.000 0.948 0.052
#> GSM152969 2 0.7016 0.497 0.116 0.728 0.156
#> GSM152970 2 0.7505 0.420 0.160 0.696 0.144
#> GSM152971 2 0.7072 0.490 0.116 0.724 0.160
#> GSM152972 2 0.7381 0.451 0.132 0.704 0.164
#> GSM152973 2 0.2955 0.699 0.008 0.912 0.080
#> GSM152974 2 0.2902 0.727 0.016 0.920 0.064
#> GSM152975 2 0.3554 0.708 0.036 0.900 0.064
#> GSM152976 2 0.6573 0.535 0.104 0.756 0.140
#> GSM152977 2 0.6091 0.573 0.092 0.784 0.124
#> GSM152978 2 0.6935 0.503 0.096 0.728 0.176
#> GSM152979 2 0.2711 0.682 0.000 0.912 0.088
#> GSM152980 2 0.3966 0.690 0.024 0.876 0.100
#> GSM152981 2 0.5760 0.115 0.000 0.672 0.328
#> GSM152982 2 0.6091 0.573 0.092 0.784 0.124
#> GSM152983 2 0.7016 0.485 0.116 0.728 0.156
#> GSM152984 2 0.2711 0.698 0.000 0.912 0.088
#> GSM152985 2 0.7545 0.429 0.136 0.692 0.172
#> GSM152986 2 0.7327 0.459 0.132 0.708 0.160
#> GSM152987 1 0.8808 0.297 0.484 0.116 0.400
#> GSM152988 2 0.3181 0.726 0.024 0.912 0.064
#> GSM152989 2 0.7265 0.464 0.128 0.712 0.160
#> GSM152990 2 0.2261 0.706 0.000 0.932 0.068
#> GSM152991 2 0.1453 0.730 0.008 0.968 0.024
#> GSM187524 1 0.2356 0.929 0.928 0.000 0.072
#> GSM187525 1 0.2356 0.929 0.928 0.000 0.072
#> GSM187526 1 0.1860 0.940 0.948 0.000 0.052
#> GSM187527 1 0.0661 0.962 0.988 0.004 0.008
#> GSM152856 1 0.0983 0.961 0.980 0.004 0.016
#> GSM152857 1 0.0983 0.961 0.980 0.004 0.016
#> GSM152858 1 0.0475 0.963 0.992 0.004 0.004
#> GSM152859 1 0.4802 0.860 0.824 0.020 0.156
#> GSM152860 1 0.0475 0.963 0.992 0.004 0.004
#> GSM152861 1 0.0475 0.963 0.992 0.004 0.004
#> GSM152862 1 0.0475 0.963 0.992 0.004 0.004
#> GSM152863 1 0.0661 0.962 0.988 0.004 0.008
#> GSM152864 1 0.0475 0.963 0.992 0.004 0.004
#> GSM152865 1 0.0475 0.963 0.992 0.004 0.004
#> GSM152866 1 0.0747 0.959 0.984 0.000 0.016
#> GSM152867 1 0.0475 0.963 0.992 0.004 0.004
#> GSM152868 1 0.0475 0.963 0.992 0.004 0.004
#> GSM152869 1 0.0475 0.963 0.992 0.004 0.004
#> GSM152870 1 0.0475 0.963 0.992 0.004 0.004
#> GSM152871 1 0.0475 0.963 0.992 0.004 0.004
#> GSM152872 1 0.0475 0.963 0.992 0.004 0.004
#> GSM152873 1 0.0747 0.959 0.984 0.000 0.016
#> GSM152874 1 0.0747 0.959 0.984 0.000 0.016
#> GSM152875 1 0.0747 0.959 0.984 0.000 0.016
#> GSM152876 1 0.0983 0.961 0.980 0.004 0.016
#> GSM152877 1 0.0747 0.959 0.984 0.000 0.016
#> GSM152878 1 0.0747 0.959 0.984 0.000 0.016
#> GSM152879 1 0.0983 0.961 0.980 0.004 0.016
#> GSM152880 1 0.0983 0.961 0.980 0.004 0.016
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.2101 0.731 0.000 0.928 0.012 0.060
#> GSM152805 3 0.4781 0.896 0.000 0.336 0.660 0.004
#> GSM152806 3 0.4761 0.895 0.000 0.332 0.664 0.004
#> GSM152807 2 0.2048 0.726 0.000 0.928 0.008 0.064
#> GSM152808 3 0.4761 0.895 0.000 0.332 0.664 0.004
#> GSM152809 2 0.2198 0.725 0.000 0.920 0.008 0.072
#> GSM152810 3 0.7563 0.590 0.008 0.400 0.444 0.148
#> GSM152811 2 0.6442 -0.660 0.008 0.476 0.468 0.048
#> GSM152812 2 0.2124 0.726 0.000 0.924 0.008 0.068
#> GSM152813 2 0.2319 0.728 0.000 0.924 0.040 0.036
#> GSM152814 2 0.2124 0.731 0.000 0.932 0.028 0.040
#> GSM152815 2 0.2198 0.724 0.000 0.920 0.008 0.072
#> GSM152816 2 0.4054 0.565 0.000 0.796 0.188 0.016
#> GSM152817 3 0.4761 0.895 0.000 0.332 0.664 0.004
#> GSM152818 3 0.4781 0.896 0.000 0.336 0.660 0.004
#> GSM152819 2 0.4428 0.369 0.000 0.720 0.276 0.004
#> GSM152820 2 0.3674 0.720 0.000 0.848 0.036 0.116
#> GSM152821 2 0.2500 0.727 0.000 0.916 0.044 0.040
#> GSM153115 2 0.4964 0.595 0.028 0.716 0.000 0.256
#> GSM153116 3 0.5050 0.839 0.000 0.408 0.588 0.004
#> GSM153117 2 0.4454 0.263 0.000 0.692 0.308 0.000
#> GSM153118 2 0.2319 0.732 0.000 0.924 0.036 0.040
#> GSM153119 2 0.6024 -0.421 0.000 0.540 0.416 0.044
#> GSM153120 2 0.5474 0.552 0.032 0.672 0.004 0.292
#> GSM153121 2 0.4472 0.509 0.000 0.760 0.220 0.020
#> GSM153122 3 0.6155 0.773 0.000 0.412 0.536 0.052
#> GSM153123 2 0.3672 0.621 0.000 0.824 0.164 0.012
#> GSM153124 2 0.4604 0.670 0.008 0.784 0.028 0.180
#> GSM153125 2 0.4737 0.607 0.020 0.728 0.000 0.252
#> GSM153126 2 0.4361 0.531 0.000 0.772 0.208 0.020
#> GSM153127 2 0.2271 0.723 0.000 0.916 0.008 0.076
#> GSM153128 2 0.4675 0.427 0.000 0.736 0.244 0.020
#> GSM153129 2 0.2843 0.696 0.000 0.892 0.088 0.020
#> GSM153130 2 0.4204 0.557 0.000 0.788 0.192 0.020
#> GSM153131 2 0.3166 0.665 0.000 0.868 0.116 0.016
#> GSM153132 2 0.2675 0.686 0.000 0.892 0.100 0.008
#> GSM153133 2 0.1635 0.721 0.000 0.948 0.044 0.008
#> GSM153134 2 0.2987 0.681 0.000 0.880 0.104 0.016
#> GSM153135 2 0.2124 0.725 0.000 0.924 0.008 0.068
#> GSM153136 2 0.5105 0.579 0.028 0.696 0.000 0.276
#> GSM153137 2 0.2922 0.718 0.004 0.884 0.008 0.104
#> GSM153138 2 0.2256 0.733 0.000 0.924 0.020 0.056
#> GSM153139 2 0.4204 0.557 0.000 0.788 0.192 0.020
#> GSM153140 2 0.2915 0.733 0.000 0.892 0.028 0.080
#> GSM153141 2 0.2342 0.722 0.000 0.912 0.008 0.080
#> GSM153142 3 0.5050 0.839 0.000 0.408 0.588 0.004
#> GSM153143 2 0.1978 0.730 0.000 0.928 0.004 0.068
#> GSM153144 2 0.3080 0.688 0.000 0.880 0.096 0.024
#> GSM153145 3 0.4761 0.895 0.000 0.332 0.664 0.004
#> GSM153146 2 0.2670 0.730 0.000 0.908 0.040 0.052
#> GSM153147 2 0.3718 0.609 0.000 0.820 0.168 0.012
#> GSM153148 2 0.2271 0.723 0.000 0.916 0.008 0.076
#> GSM153149 2 0.2174 0.733 0.000 0.928 0.020 0.052
#> GSM153150 2 0.5085 0.592 0.032 0.708 0.000 0.260
#> GSM153151 2 0.3659 0.657 0.000 0.840 0.136 0.024
#> GSM153152 2 0.2101 0.711 0.000 0.928 0.060 0.012
#> GSM153153 2 0.1706 0.725 0.000 0.948 0.036 0.016
#> GSM153154 2 0.3052 0.660 0.000 0.860 0.136 0.004
#> GSM153155 2 0.2521 0.717 0.000 0.912 0.064 0.024
#> GSM153156 2 0.4436 0.519 0.000 0.764 0.216 0.020
#> GSM153157 2 0.4936 0.149 0.000 0.672 0.316 0.012
#> GSM153158 2 0.4985 -0.529 0.000 0.532 0.468 0.000
#> GSM153159 3 0.5039 0.843 0.000 0.404 0.592 0.004
#> GSM153160 2 0.4542 0.490 0.000 0.752 0.228 0.020
#> GSM153161 2 0.2480 0.723 0.000 0.904 0.008 0.088
#> GSM153162 2 0.2861 0.683 0.000 0.888 0.096 0.016
#> GSM153163 2 0.3925 0.590 0.000 0.808 0.176 0.016
#> GSM153164 2 0.5328 0.523 0.000 0.724 0.212 0.064
#> GSM153165 2 0.3900 0.604 0.000 0.816 0.164 0.020
#> GSM153166 2 0.2224 0.727 0.000 0.928 0.040 0.032
#> GSM153167 2 0.2805 0.686 0.000 0.888 0.100 0.012
#> GSM153168 3 0.4741 0.889 0.000 0.328 0.668 0.004
#> GSM153169 2 0.3764 0.608 0.000 0.816 0.172 0.012
#> GSM153170 2 0.3806 0.615 0.000 0.824 0.156 0.020
#> GSM153171 2 0.5664 0.626 0.036 0.728 0.032 0.204
#> GSM153172 2 0.2131 0.728 0.000 0.932 0.036 0.032
#> GSM153173 2 0.3900 0.604 0.000 0.816 0.164 0.020
#> GSM153174 2 0.2973 0.682 0.000 0.884 0.096 0.020
#> GSM153175 2 0.5098 0.636 0.024 0.744 0.016 0.216
#> GSM153176 2 0.5018 0.640 0.012 0.744 0.024 0.220
#> GSM153177 2 0.2676 0.698 0.000 0.896 0.092 0.012
#> GSM152931 2 0.4838 0.605 0.024 0.724 0.000 0.252
#> GSM152932 2 0.2124 0.732 0.000 0.932 0.040 0.028
#> GSM152933 2 0.2443 0.719 0.000 0.916 0.060 0.024
#> GSM152934 2 0.4247 0.710 0.016 0.836 0.044 0.104
#> GSM152935 2 0.4610 0.488 0.000 0.744 0.236 0.020
#> GSM152936 2 0.4986 0.631 0.020 0.740 0.012 0.228
#> GSM152937 2 0.4163 0.573 0.000 0.792 0.188 0.020
#> GSM152938 2 0.4163 0.573 0.000 0.792 0.188 0.020
#> GSM152939 2 0.4322 0.649 0.000 0.804 0.152 0.044
#> GSM152940 2 0.5717 0.499 0.044 0.632 0.000 0.324
#> GSM152941 1 0.5479 0.634 0.740 0.052 0.016 0.192
#> GSM152942 2 0.3384 0.678 0.000 0.860 0.116 0.024
#> GSM152943 2 0.2706 0.729 0.000 0.900 0.020 0.080
#> GSM152944 2 0.3606 0.644 0.000 0.840 0.140 0.020
#> GSM152945 4 0.7349 0.306 0.000 0.164 0.364 0.472
#> GSM152946 2 0.4288 0.700 0.008 0.824 0.044 0.124
#> GSM152947 2 0.5649 0.560 0.044 0.672 0.004 0.280
#> GSM152948 2 0.2021 0.729 0.000 0.932 0.012 0.056
#> GSM152949 2 0.2741 0.684 0.000 0.892 0.096 0.012
#> GSM152950 2 0.1902 0.714 0.000 0.932 0.064 0.004
#> GSM152951 2 0.2275 0.732 0.004 0.928 0.020 0.048
#> GSM152952 2 0.2125 0.724 0.000 0.920 0.004 0.076
#> GSM152953 2 0.2179 0.728 0.000 0.924 0.012 0.064
#> GSM152954 2 0.5088 0.573 0.024 0.688 0.000 0.288
#> GSM152955 2 0.5085 0.424 0.000 0.708 0.260 0.032
#> GSM152956 2 0.2271 0.723 0.000 0.916 0.008 0.076
#> GSM152957 2 0.5088 0.587 0.020 0.700 0.004 0.276
#> GSM152958 2 0.5131 0.574 0.028 0.692 0.000 0.280
#> GSM152959 2 0.5334 0.573 0.028 0.684 0.004 0.284
#> GSM152960 2 0.5222 0.573 0.032 0.688 0.000 0.280
#> GSM152961 2 0.5430 0.545 0.036 0.664 0.000 0.300
#> GSM152962 2 0.3958 0.620 0.000 0.816 0.160 0.024
#> GSM152963 2 0.2271 0.724 0.000 0.916 0.008 0.076
#> GSM152964 3 0.6111 0.844 0.000 0.392 0.556 0.052
#> GSM152965 2 0.1820 0.729 0.000 0.944 0.036 0.020
#> GSM152966 2 0.4868 0.602 0.024 0.720 0.000 0.256
#> GSM152967 2 0.2021 0.720 0.000 0.936 0.040 0.024
#> GSM152968 2 0.2987 0.677 0.000 0.880 0.104 0.016
#> GSM152969 2 0.4868 0.599 0.024 0.720 0.000 0.256
#> GSM152970 2 0.5623 0.561 0.044 0.676 0.004 0.276
#> GSM152971 2 0.4855 0.596 0.020 0.712 0.000 0.268
#> GSM152972 2 0.5131 0.574 0.028 0.692 0.000 0.280
#> GSM152973 2 0.4194 0.612 0.000 0.800 0.172 0.028
#> GSM152974 2 0.2408 0.731 0.000 0.920 0.036 0.044
#> GSM152975 2 0.3082 0.727 0.000 0.884 0.032 0.084
#> GSM152976 2 0.5010 0.620 0.016 0.728 0.012 0.244
#> GSM152977 2 0.5184 0.640 0.012 0.732 0.028 0.228
#> GSM152978 2 0.4635 0.604 0.012 0.720 0.000 0.268
#> GSM152979 2 0.4035 0.591 0.000 0.804 0.176 0.020
#> GSM152980 2 0.3638 0.718 0.000 0.848 0.032 0.120
#> GSM152981 3 0.4741 0.889 0.000 0.328 0.668 0.004
#> GSM152982 2 0.5184 0.640 0.012 0.732 0.028 0.228
#> GSM152983 2 0.5171 0.593 0.020 0.704 0.008 0.268
#> GSM152984 2 0.3910 0.625 0.000 0.820 0.156 0.024
#> GSM152985 2 0.5272 0.563 0.032 0.680 0.000 0.288
#> GSM152986 2 0.5105 0.579 0.028 0.696 0.000 0.276
#> GSM152987 4 0.7871 0.116 0.380 0.040 0.108 0.472
#> GSM152988 2 0.3900 0.708 0.000 0.844 0.084 0.072
#> GSM152989 2 0.5188 0.582 0.024 0.696 0.004 0.276
#> GSM152990 2 0.3547 0.642 0.000 0.840 0.144 0.016
#> GSM152991 2 0.2179 0.717 0.000 0.924 0.064 0.012
#> GSM187524 1 0.3757 0.830 0.828 0.000 0.020 0.152
#> GSM187525 1 0.3757 0.830 0.828 0.000 0.020 0.152
#> GSM187526 1 0.3443 0.848 0.848 0.000 0.016 0.136
#> GSM187527 1 0.1118 0.899 0.964 0.000 0.000 0.036
#> GSM152856 1 0.0921 0.894 0.972 0.000 0.000 0.028
#> GSM152857 1 0.0921 0.894 0.972 0.000 0.000 0.028
#> GSM152858 1 0.1940 0.905 0.924 0.000 0.000 0.076
#> GSM152859 1 0.5545 0.671 0.736 0.008 0.076 0.180
#> GSM152860 1 0.1940 0.905 0.924 0.000 0.000 0.076
#> GSM152861 1 0.2011 0.902 0.920 0.000 0.000 0.080
#> GSM152862 1 0.1940 0.905 0.924 0.000 0.000 0.076
#> GSM152863 1 0.0707 0.901 0.980 0.000 0.000 0.020
#> GSM152864 1 0.1940 0.905 0.924 0.000 0.000 0.076
#> GSM152865 1 0.1940 0.905 0.924 0.000 0.000 0.076
#> GSM152866 1 0.0921 0.894 0.972 0.000 0.000 0.028
#> GSM152867 1 0.1940 0.905 0.924 0.000 0.000 0.076
#> GSM152868 1 0.1940 0.905 0.924 0.000 0.000 0.076
#> GSM152869 1 0.1940 0.905 0.924 0.000 0.000 0.076
#> GSM152870 1 0.1940 0.905 0.924 0.000 0.000 0.076
#> GSM152871 1 0.1940 0.905 0.924 0.000 0.000 0.076
#> GSM152872 1 0.1940 0.905 0.924 0.000 0.000 0.076
#> GSM152873 1 0.1022 0.893 0.968 0.000 0.000 0.032
#> GSM152874 1 0.1022 0.893 0.968 0.000 0.000 0.032
#> GSM152875 1 0.1022 0.893 0.968 0.000 0.000 0.032
#> GSM152876 1 0.0921 0.894 0.972 0.000 0.000 0.028
#> GSM152877 1 0.1022 0.893 0.968 0.000 0.000 0.032
#> GSM152878 1 0.1022 0.893 0.968 0.000 0.000 0.032
#> GSM152879 1 0.0921 0.894 0.972 0.000 0.000 0.028
#> GSM152880 1 0.0921 0.894 0.972 0.000 0.000 0.028
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.1758 0.7569 0.004 0.944 0.008 NA 0.020
#> GSM152805 5 0.2929 0.7849 0.000 0.152 0.008 NA 0.840
#> GSM152806 5 0.2798 0.7780 0.000 0.140 0.008 NA 0.852
#> GSM152807 2 0.1187 0.7509 0.004 0.964 0.004 NA 0.004
#> GSM152808 5 0.2798 0.7780 0.000 0.140 0.008 NA 0.852
#> GSM152809 2 0.1363 0.7498 0.004 0.956 0.004 NA 0.004
#> GSM152810 5 0.6925 0.5036 0.008 0.292 0.008 NA 0.484
#> GSM152811 5 0.5813 0.6509 0.008 0.324 0.008 NA 0.592
#> GSM152812 2 0.1277 0.7507 0.004 0.960 0.004 NA 0.004
#> GSM152813 2 0.2297 0.7555 0.000 0.912 0.008 NA 0.060
#> GSM152814 2 0.2213 0.7571 0.004 0.920 0.004 NA 0.048
#> GSM152815 2 0.1363 0.7496 0.004 0.956 0.004 NA 0.004
#> GSM152816 2 0.4347 0.5864 0.000 0.716 0.004 NA 0.256
#> GSM152817 5 0.2798 0.7780 0.000 0.140 0.008 NA 0.852
#> GSM152818 5 0.2929 0.7849 0.000 0.152 0.008 NA 0.840
#> GSM152819 2 0.4457 0.3623 0.000 0.620 0.000 NA 0.368
#> GSM152820 2 0.3684 0.7483 0.000 0.824 0.004 NA 0.056
#> GSM152821 2 0.2484 0.7540 0.000 0.900 0.004 NA 0.068
#> GSM153115 2 0.4558 0.6252 0.064 0.728 0.000 NA 0.000
#> GSM153116 5 0.3890 0.7624 0.000 0.252 0.012 NA 0.736
#> GSM153117 2 0.4436 0.3180 0.000 0.596 0.000 NA 0.396
#> GSM153118 2 0.2172 0.7590 0.004 0.916 0.000 NA 0.060
#> GSM153119 5 0.6384 0.5364 0.000 0.360 0.092 NA 0.520
#> GSM153120 2 0.5817 0.5612 0.072 0.672 0.040 NA 0.004
#> GSM153121 2 0.5266 0.5613 0.000 0.684 0.020 NA 0.236
#> GSM153122 5 0.5711 0.6973 0.000 0.196 0.096 NA 0.676
#> GSM153123 2 0.4481 0.6581 0.000 0.760 0.012 NA 0.176
#> GSM153124 2 0.4126 0.6965 0.032 0.800 0.000 NA 0.028
#> GSM153125 2 0.4555 0.6357 0.060 0.740 0.000 NA 0.004
#> GSM153126 2 0.5212 0.5744 0.000 0.692 0.020 NA 0.228
#> GSM153127 2 0.1446 0.7485 0.004 0.952 0.004 NA 0.004
#> GSM153128 2 0.4999 0.4359 0.004 0.640 0.004 NA 0.320
#> GSM153129 2 0.3351 0.7270 0.000 0.836 0.004 NA 0.132
#> GSM153130 2 0.4943 0.6055 0.000 0.716 0.016 NA 0.212
#> GSM153131 2 0.3811 0.7020 0.000 0.808 0.008 NA 0.148
#> GSM153132 2 0.3283 0.7171 0.000 0.832 0.000 NA 0.140
#> GSM153133 2 0.2522 0.7465 0.000 0.896 0.004 NA 0.076
#> GSM153134 2 0.3567 0.7127 0.000 0.820 0.004 NA 0.144
#> GSM153135 2 0.1277 0.7503 0.004 0.960 0.004 NA 0.004
#> GSM153136 2 0.4701 0.6138 0.076 0.720 0.000 NA 0.000
#> GSM153137 2 0.2471 0.7435 0.016 0.908 0.012 NA 0.004
#> GSM153138 2 0.2443 0.7585 0.004 0.912 0.008 NA 0.040
#> GSM153139 2 0.4943 0.6055 0.000 0.716 0.016 NA 0.212
#> GSM153140 2 0.3666 0.7587 0.012 0.844 0.004 NA 0.064
#> GSM153141 2 0.1526 0.7474 0.004 0.948 0.004 NA 0.004
#> GSM153142 5 0.3916 0.7591 0.000 0.256 0.012 NA 0.732
#> GSM153143 2 0.1605 0.7544 0.004 0.944 0.000 NA 0.012
#> GSM153144 2 0.3635 0.7155 0.000 0.824 0.008 NA 0.132
#> GSM153145 5 0.2798 0.7780 0.000 0.140 0.008 NA 0.852
#> GSM153146 2 0.2353 0.7579 0.004 0.908 0.000 NA 0.060
#> GSM153147 2 0.4584 0.6522 0.000 0.752 0.016 NA 0.184
#> GSM153148 2 0.1446 0.7485 0.004 0.952 0.004 NA 0.004
#> GSM153149 2 0.1828 0.7586 0.000 0.936 0.004 NA 0.028
#> GSM153150 2 0.4910 0.6231 0.080 0.712 0.000 NA 0.004
#> GSM153151 2 0.4483 0.6884 0.000 0.772 0.020 NA 0.156
#> GSM153152 2 0.3008 0.7384 0.000 0.868 0.004 NA 0.092
#> GSM153153 2 0.2110 0.7527 0.000 0.912 0.000 NA 0.072
#> GSM153154 2 0.3639 0.6959 0.000 0.792 0.000 NA 0.184
#> GSM153155 2 0.2983 0.7445 0.000 0.868 0.004 NA 0.096
#> GSM153156 2 0.5240 0.5687 0.000 0.688 0.020 NA 0.232
#> GSM153157 2 0.4989 0.0661 0.000 0.552 0.000 NA 0.416
#> GSM153158 5 0.4350 0.4940 0.000 0.408 0.004 NA 0.588
#> GSM153159 5 0.4271 0.7605 0.000 0.252 0.012 NA 0.724
#> GSM153160 2 0.5368 0.5365 0.000 0.668 0.020 NA 0.252
#> GSM153161 2 0.1877 0.7484 0.004 0.932 0.008 NA 0.004
#> GSM153162 2 0.3601 0.7107 0.000 0.824 0.008 NA 0.136
#> GSM153163 2 0.4654 0.6369 0.000 0.740 0.012 NA 0.196
#> GSM153164 2 0.5159 0.5302 0.000 0.644 0.000 NA 0.284
#> GSM153165 2 0.4583 0.6454 0.000 0.748 0.016 NA 0.192
#> GSM153166 2 0.2079 0.7548 0.000 0.916 0.000 NA 0.064
#> GSM153167 2 0.3366 0.7167 0.000 0.828 0.000 NA 0.140
#> GSM153168 5 0.2753 0.7715 0.000 0.136 0.008 NA 0.856
#> GSM153169 2 0.4547 0.6451 0.000 0.744 0.008 NA 0.196
#> GSM153170 2 0.4514 0.6544 0.000 0.756 0.016 NA 0.184
#> GSM153171 2 0.5251 0.6601 0.068 0.724 0.000 NA 0.040
#> GSM153172 2 0.2103 0.7550 0.000 0.920 0.004 NA 0.056
#> GSM153173 2 0.4583 0.6454 0.000 0.748 0.016 NA 0.192
#> GSM153174 2 0.3711 0.7098 0.000 0.820 0.012 NA 0.136
#> GSM153175 2 0.4704 0.6666 0.044 0.748 0.004 NA 0.016
#> GSM153176 2 0.4901 0.6694 0.048 0.752 0.004 NA 0.032
#> GSM153177 2 0.3152 0.7277 0.000 0.840 0.000 NA 0.136
#> GSM152931 2 0.4434 0.6339 0.056 0.736 0.000 NA 0.000
#> GSM152932 2 0.2234 0.7582 0.004 0.916 0.004 NA 0.060
#> GSM152933 2 0.2550 0.7469 0.000 0.892 0.004 NA 0.084
#> GSM152934 2 0.4085 0.7425 0.052 0.824 0.000 NA 0.068
#> GSM152935 2 0.5277 0.5127 0.000 0.660 0.036 NA 0.276
#> GSM152936 2 0.4681 0.6619 0.056 0.748 0.000 NA 0.016
#> GSM152937 2 0.5036 0.6138 0.000 0.716 0.020 NA 0.204
#> GSM152938 2 0.5036 0.6138 0.000 0.716 0.020 NA 0.204
#> GSM152939 2 0.4913 0.6867 0.004 0.744 0.016 NA 0.168
#> GSM152940 2 0.5613 0.5337 0.096 0.648 0.012 NA 0.000
#> GSM152941 1 0.4440 0.4795 0.776 0.060 0.000 NA 0.016
#> GSM152942 2 0.4085 0.7112 0.004 0.796 0.008 NA 0.152
#> GSM152943 2 0.2652 0.7536 0.004 0.904 0.024 NA 0.020
#> GSM152944 2 0.4296 0.6832 0.000 0.776 0.016 NA 0.168
#> GSM152945 3 0.2036 0.6388 0.000 0.028 0.928 NA 0.036
#> GSM152946 2 0.4171 0.7327 0.024 0.816 0.004 NA 0.060
#> GSM152947 2 0.5209 0.5868 0.072 0.680 0.004 NA 0.004
#> GSM152948 2 0.1267 0.7541 0.000 0.960 0.004 NA 0.012
#> GSM152949 2 0.3556 0.7120 0.000 0.828 0.008 NA 0.132
#> GSM152950 2 0.2953 0.7401 0.000 0.868 0.004 NA 0.100
#> GSM152951 2 0.1725 0.7580 0.004 0.944 0.004 NA 0.024
#> GSM152952 2 0.1430 0.7502 0.000 0.944 0.000 NA 0.004
#> GSM152953 2 0.1686 0.7541 0.004 0.944 0.004 NA 0.012
#> GSM152954 2 0.4734 0.6063 0.064 0.704 0.000 NA 0.000
#> GSM152955 2 0.5176 0.4376 0.004 0.628 0.012 NA 0.328
#> GSM152956 2 0.1446 0.7485 0.004 0.952 0.004 NA 0.004
#> GSM152957 2 0.4952 0.6136 0.068 0.708 0.000 NA 0.008
#> GSM152958 2 0.4736 0.6050 0.072 0.712 0.000 NA 0.000
#> GSM152959 2 0.4803 0.6109 0.064 0.712 0.000 NA 0.004
#> GSM152960 2 0.4708 0.6077 0.068 0.712 0.000 NA 0.000
#> GSM152961 2 0.5040 0.5743 0.084 0.680 0.000 NA 0.000
#> GSM152962 2 0.4583 0.6537 0.000 0.748 0.016 NA 0.192
#> GSM152963 2 0.1730 0.7486 0.004 0.940 0.004 NA 0.008
#> GSM152964 5 0.5422 0.7402 0.000 0.196 0.108 NA 0.684
#> GSM152965 2 0.2331 0.7554 0.000 0.908 0.004 NA 0.064
#> GSM152966 2 0.4588 0.6326 0.060 0.736 0.000 NA 0.004
#> GSM152967 2 0.2734 0.7491 0.000 0.888 0.008 NA 0.076
#> GSM152968 2 0.3755 0.7065 0.000 0.816 0.012 NA 0.140
#> GSM152969 2 0.4649 0.6288 0.064 0.732 0.000 NA 0.004
#> GSM152970 2 0.5314 0.5922 0.100 0.684 0.000 NA 0.008
#> GSM152971 2 0.4558 0.6220 0.064 0.728 0.000 NA 0.000
#> GSM152972 2 0.4766 0.6015 0.072 0.708 0.000 NA 0.000
#> GSM152973 2 0.4939 0.6576 0.004 0.732 0.016 NA 0.192
#> GSM152974 2 0.1918 0.7577 0.004 0.932 0.004 NA 0.048
#> GSM152975 2 0.3488 0.7528 0.016 0.852 0.000 NA 0.064
#> GSM152976 2 0.4841 0.6451 0.064 0.736 0.000 NA 0.016
#> GSM152977 2 0.5056 0.6674 0.060 0.736 0.000 NA 0.036
#> GSM152978 2 0.4450 0.6344 0.044 0.736 0.004 NA 0.000
#> GSM152979 2 0.4910 0.6318 0.000 0.728 0.020 NA 0.196
#> GSM152980 2 0.3664 0.7468 0.000 0.824 0.004 NA 0.052
#> GSM152981 5 0.2753 0.7715 0.000 0.136 0.008 NA 0.856
#> GSM152982 2 0.5056 0.6674 0.060 0.736 0.000 NA 0.036
#> GSM152983 2 0.4969 0.6198 0.064 0.712 0.000 NA 0.012
#> GSM152984 2 0.4766 0.6656 0.000 0.748 0.020 NA 0.172
#> GSM152985 2 0.4879 0.5909 0.076 0.696 0.000 NA 0.000
#> GSM152986 2 0.4736 0.6059 0.072 0.712 0.000 NA 0.000
#> GSM152987 3 0.7764 0.5495 0.248 0.024 0.412 NA 0.024
#> GSM152988 2 0.4614 0.7346 0.012 0.784 0.012 NA 0.116
#> GSM152989 2 0.5009 0.6092 0.072 0.704 0.000 NA 0.008
#> GSM152990 2 0.4406 0.6727 0.000 0.768 0.016 NA 0.172
#> GSM152991 2 0.2625 0.7435 0.000 0.876 0.000 NA 0.108
#> GSM187524 1 0.2771 0.6589 0.860 0.000 0.000 NA 0.012
#> GSM187525 1 0.2771 0.6589 0.860 0.000 0.000 NA 0.012
#> GSM187526 1 0.2470 0.6819 0.884 0.000 0.000 NA 0.012
#> GSM187527 1 0.5188 0.6911 0.636 0.000 0.008 NA 0.048
#> GSM152856 1 0.5272 0.6855 0.616 0.000 0.008 NA 0.048
#> GSM152857 1 0.5272 0.6855 0.616 0.000 0.008 NA 0.048
#> GSM152858 1 0.0000 0.7490 1.000 0.000 0.000 NA 0.000
#> GSM152859 1 0.4548 0.5087 0.728 0.004 0.004 NA 0.036
#> GSM152860 1 0.0000 0.7490 1.000 0.000 0.000 NA 0.000
#> GSM152861 1 0.0162 0.7467 0.996 0.000 0.000 NA 0.000
#> GSM152862 1 0.0000 0.7490 1.000 0.000 0.000 NA 0.000
#> GSM152863 1 0.3053 0.7326 0.828 0.000 0.000 NA 0.008
#> GSM152864 1 0.0510 0.7526 0.984 0.000 0.000 NA 0.000
#> GSM152865 1 0.0510 0.7526 0.984 0.000 0.000 NA 0.000
#> GSM152866 1 0.5205 0.6909 0.632 0.000 0.008 NA 0.048
#> GSM152867 1 0.0510 0.7526 0.984 0.000 0.000 NA 0.000
#> GSM152868 1 0.0510 0.7526 0.984 0.000 0.000 NA 0.000
#> GSM152869 1 0.0510 0.7526 0.984 0.000 0.000 NA 0.000
#> GSM152870 1 0.0000 0.7490 1.000 0.000 0.000 NA 0.000
#> GSM152871 1 0.0000 0.7490 1.000 0.000 0.000 NA 0.000
#> GSM152872 1 0.0000 0.7490 1.000 0.000 0.000 NA 0.000
#> GSM152873 1 0.5287 0.6840 0.612 0.000 0.008 NA 0.048
#> GSM152874 1 0.5287 0.6840 0.612 0.000 0.008 NA 0.048
#> GSM152875 1 0.5287 0.6840 0.612 0.000 0.008 NA 0.048
#> GSM152876 1 0.5272 0.6855 0.616 0.000 0.008 NA 0.048
#> GSM152877 1 0.5287 0.6840 0.612 0.000 0.008 NA 0.048
#> GSM152878 1 0.5287 0.6840 0.612 0.000 0.008 NA 0.048
#> GSM152879 1 0.5272 0.6855 0.616 0.000 0.008 NA 0.048
#> GSM152880 1 0.5272 0.6855 0.616 0.000 0.008 NA 0.048
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.1745 0.744 0.000 0.920 0.068 0.000 0.012 0.000
#> GSM152805 5 0.1814 0.753 0.000 0.100 0.000 0.000 0.900 0.000
#> GSM152806 5 0.1663 0.747 0.000 0.088 0.000 0.000 0.912 0.000
#> GSM152807 2 0.1411 0.738 0.000 0.936 0.060 0.000 0.004 0.000
#> GSM152808 5 0.1663 0.747 0.000 0.088 0.000 0.000 0.912 0.000
#> GSM152809 2 0.1531 0.737 0.000 0.928 0.068 0.000 0.004 0.000
#> GSM152810 5 0.7265 0.327 0.212 0.224 0.120 0.004 0.440 0.000
#> GSM152811 5 0.6086 0.551 0.056 0.256 0.108 0.004 0.576 0.000
#> GSM152812 2 0.1411 0.737 0.000 0.936 0.060 0.000 0.004 0.000
#> GSM152813 2 0.2129 0.744 0.000 0.904 0.056 0.000 0.040 0.000
#> GSM152814 2 0.1789 0.744 0.000 0.924 0.044 0.000 0.032 0.000
#> GSM152815 2 0.1471 0.736 0.000 0.932 0.064 0.000 0.004 0.000
#> GSM152816 2 0.4587 0.585 0.000 0.688 0.108 0.000 0.204 0.000
#> GSM152817 5 0.1663 0.747 0.000 0.088 0.000 0.000 0.912 0.000
#> GSM152818 5 0.1814 0.753 0.000 0.100 0.000 0.000 0.900 0.000
#> GSM152819 2 0.4760 0.405 0.000 0.604 0.068 0.000 0.328 0.000
#> GSM152820 2 0.3394 0.736 0.000 0.776 0.200 0.000 0.024 0.000
#> GSM152821 2 0.2066 0.743 0.000 0.904 0.072 0.000 0.024 0.000
#> GSM153115 2 0.4152 0.613 0.032 0.664 0.304 0.000 0.000 0.000
#> GSM153116 5 0.3152 0.718 0.000 0.196 0.008 0.004 0.792 0.000
#> GSM153117 2 0.4500 0.319 0.000 0.572 0.036 0.000 0.392 0.000
#> GSM153118 2 0.2122 0.747 0.000 0.900 0.076 0.000 0.024 0.000
#> GSM153119 5 0.6575 0.504 0.016 0.316 0.084 0.076 0.508 0.000
#> GSM153120 2 0.5196 0.548 0.068 0.600 0.312 0.020 0.000 0.000
#> GSM153121 2 0.5114 0.549 0.004 0.636 0.224 0.000 0.136 0.000
#> GSM153122 5 0.5598 0.610 0.024 0.132 0.072 0.080 0.692 0.000
#> GSM153123 2 0.4311 0.637 0.000 0.716 0.196 0.000 0.088 0.000
#> GSM153124 2 0.3852 0.680 0.016 0.732 0.240 0.000 0.012 0.000
#> GSM153125 2 0.4165 0.623 0.028 0.676 0.292 0.000 0.004 0.000
#> GSM153126 2 0.4994 0.561 0.004 0.648 0.228 0.000 0.120 0.000
#> GSM153127 2 0.1531 0.735 0.000 0.928 0.068 0.000 0.004 0.000
#> GSM153128 2 0.5422 0.435 0.004 0.588 0.156 0.000 0.252 0.000
#> GSM153129 2 0.3370 0.717 0.000 0.812 0.124 0.000 0.064 0.000
#> GSM153130 2 0.4883 0.592 0.004 0.664 0.216 0.000 0.116 0.000
#> GSM153131 2 0.3930 0.687 0.004 0.768 0.156 0.000 0.072 0.000
#> GSM153132 2 0.3767 0.699 0.004 0.788 0.128 0.000 0.080 0.000
#> GSM153133 2 0.2527 0.734 0.000 0.876 0.084 0.000 0.040 0.000
#> GSM153134 2 0.3782 0.699 0.004 0.784 0.140 0.000 0.072 0.000
#> GSM153135 2 0.1531 0.736 0.000 0.928 0.068 0.000 0.004 0.000
#> GSM153136 2 0.4368 0.606 0.048 0.656 0.296 0.000 0.000 0.000
#> GSM153137 2 0.2714 0.727 0.012 0.848 0.136 0.000 0.004 0.000
#> GSM153138 2 0.2301 0.747 0.000 0.884 0.096 0.000 0.020 0.000
#> GSM153139 2 0.4883 0.592 0.004 0.664 0.216 0.000 0.116 0.000
#> GSM153140 2 0.3275 0.746 0.004 0.816 0.144 0.000 0.036 0.000
#> GSM153141 2 0.1700 0.733 0.000 0.916 0.080 0.000 0.004 0.000
#> GSM153142 5 0.3183 0.714 0.000 0.200 0.008 0.004 0.788 0.000
#> GSM153143 2 0.1970 0.743 0.000 0.900 0.092 0.000 0.008 0.000
#> GSM153144 2 0.3615 0.699 0.004 0.796 0.140 0.000 0.060 0.000
#> GSM153145 5 0.1663 0.747 0.000 0.088 0.000 0.000 0.912 0.000
#> GSM153146 2 0.2145 0.746 0.000 0.900 0.072 0.000 0.028 0.000
#> GSM153147 2 0.4368 0.635 0.000 0.708 0.204 0.000 0.088 0.000
#> GSM153148 2 0.1531 0.735 0.000 0.928 0.068 0.000 0.004 0.000
#> GSM153149 2 0.1926 0.746 0.000 0.912 0.068 0.000 0.020 0.000
#> GSM153150 2 0.4368 0.614 0.048 0.656 0.296 0.000 0.000 0.000
#> GSM153151 2 0.4261 0.655 0.004 0.720 0.212 0.000 0.064 0.000
#> GSM153152 2 0.2842 0.723 0.000 0.852 0.104 0.000 0.044 0.000
#> GSM153153 2 0.2003 0.742 0.000 0.912 0.044 0.000 0.044 0.000
#> GSM153154 2 0.4293 0.674 0.004 0.740 0.112 0.000 0.144 0.000
#> GSM153155 2 0.2712 0.734 0.000 0.864 0.088 0.000 0.048 0.000
#> GSM153156 2 0.5135 0.556 0.004 0.636 0.216 0.000 0.144 0.000
#> GSM153157 2 0.5721 0.137 0.008 0.508 0.140 0.000 0.344 0.000
#> GSM153158 5 0.4446 0.488 0.000 0.368 0.028 0.004 0.600 0.000
#> GSM153159 5 0.3867 0.711 0.000 0.192 0.040 0.008 0.760 0.000
#> GSM153160 2 0.5259 0.517 0.004 0.616 0.232 0.000 0.148 0.000
#> GSM153161 2 0.2288 0.733 0.004 0.876 0.116 0.000 0.004 0.000
#> GSM153162 2 0.3672 0.693 0.004 0.792 0.140 0.000 0.064 0.000
#> GSM153163 2 0.4624 0.624 0.004 0.692 0.208 0.000 0.096 0.000
#> GSM153164 2 0.4972 0.528 0.000 0.620 0.108 0.000 0.272 0.000
#> GSM153165 2 0.4524 0.635 0.004 0.704 0.200 0.000 0.092 0.000
#> GSM153166 2 0.2197 0.743 0.000 0.900 0.056 0.000 0.044 0.000
#> GSM153167 2 0.3649 0.705 0.004 0.796 0.132 0.000 0.068 0.000
#> GSM153168 5 0.1610 0.740 0.000 0.084 0.000 0.000 0.916 0.000
#> GSM153169 2 0.4596 0.624 0.004 0.696 0.204 0.000 0.096 0.000
#> GSM153170 2 0.4431 0.643 0.004 0.712 0.200 0.000 0.084 0.000
#> GSM153171 2 0.4752 0.647 0.040 0.668 0.268 0.004 0.020 0.000
#> GSM153172 2 0.1863 0.743 0.000 0.920 0.044 0.000 0.036 0.000
#> GSM153173 2 0.4524 0.635 0.004 0.704 0.200 0.000 0.092 0.000
#> GSM153174 2 0.3710 0.692 0.004 0.788 0.144 0.000 0.064 0.000
#> GSM153175 2 0.4327 0.656 0.028 0.676 0.284 0.000 0.012 0.000
#> GSM153176 2 0.4397 0.656 0.024 0.688 0.264 0.000 0.024 0.000
#> GSM153177 2 0.3125 0.717 0.000 0.836 0.084 0.000 0.080 0.000
#> GSM152931 2 0.4117 0.624 0.032 0.672 0.296 0.000 0.000 0.000
#> GSM152932 2 0.1845 0.746 0.000 0.920 0.052 0.000 0.028 0.000
#> GSM152933 2 0.2376 0.735 0.000 0.888 0.068 0.000 0.044 0.000
#> GSM152934 2 0.3740 0.736 0.032 0.800 0.136 0.000 0.032 0.000
#> GSM152935 2 0.5298 0.484 0.004 0.624 0.088 0.016 0.268 0.000
#> GSM152936 2 0.4023 0.650 0.028 0.704 0.264 0.000 0.004 0.000
#> GSM152937 2 0.4662 0.588 0.000 0.668 0.236 0.000 0.096 0.000
#> GSM152938 2 0.4822 0.579 0.004 0.656 0.248 0.000 0.092 0.000
#> GSM152939 2 0.4354 0.672 0.000 0.704 0.216 0.000 0.080 0.000
#> GSM152940 2 0.5205 0.524 0.072 0.580 0.336 0.008 0.004 0.000
#> GSM152941 1 0.5875 0.489 0.608 0.052 0.104 0.004 0.000 0.232
#> GSM152942 2 0.3860 0.697 0.000 0.764 0.164 0.000 0.072 0.000
#> GSM152943 2 0.2933 0.737 0.004 0.848 0.124 0.008 0.016 0.000
#> GSM152944 2 0.4345 0.665 0.004 0.728 0.176 0.000 0.092 0.000
#> GSM152945 4 0.0291 0.000 0.000 0.004 0.004 0.992 0.000 0.000
#> GSM152946 2 0.3651 0.725 0.016 0.792 0.160 0.000 0.032 0.000
#> GSM152947 2 0.4794 0.573 0.048 0.608 0.336 0.004 0.000 0.004
#> GSM152948 2 0.1367 0.741 0.000 0.944 0.044 0.000 0.012 0.000
#> GSM152949 2 0.3691 0.691 0.004 0.788 0.148 0.000 0.060 0.000
#> GSM152950 2 0.2762 0.725 0.000 0.860 0.092 0.000 0.048 0.000
#> GSM152951 2 0.1590 0.745 0.008 0.936 0.048 0.000 0.008 0.000
#> GSM152952 2 0.1753 0.737 0.000 0.912 0.084 0.000 0.004 0.000
#> GSM152953 2 0.1644 0.740 0.000 0.920 0.076 0.000 0.004 0.000
#> GSM152954 2 0.4300 0.596 0.036 0.640 0.324 0.000 0.000 0.000
#> GSM152955 2 0.5052 0.423 0.000 0.592 0.084 0.004 0.320 0.000
#> GSM152956 2 0.1531 0.735 0.000 0.928 0.068 0.000 0.004 0.000
#> GSM152957 2 0.4420 0.600 0.036 0.640 0.320 0.000 0.004 0.000
#> GSM152958 2 0.4316 0.595 0.040 0.648 0.312 0.000 0.000 0.000
#> GSM152959 2 0.4299 0.605 0.040 0.652 0.308 0.000 0.000 0.000
#> GSM152960 2 0.4361 0.600 0.044 0.648 0.308 0.000 0.000 0.000
#> GSM152961 2 0.4594 0.561 0.052 0.608 0.340 0.000 0.000 0.000
#> GSM152962 2 0.4283 0.649 0.000 0.724 0.180 0.000 0.096 0.000
#> GSM152963 2 0.1644 0.735 0.000 0.920 0.076 0.000 0.004 0.000
#> GSM152964 5 0.5173 0.660 0.024 0.132 0.036 0.088 0.720 0.000
#> GSM152965 2 0.2182 0.744 0.004 0.900 0.076 0.000 0.020 0.000
#> GSM152966 2 0.4083 0.621 0.028 0.668 0.304 0.000 0.000 0.000
#> GSM152967 2 0.2506 0.737 0.000 0.880 0.068 0.000 0.052 0.000
#> GSM152968 2 0.3840 0.689 0.004 0.776 0.152 0.000 0.068 0.000
#> GSM152969 2 0.4253 0.616 0.032 0.668 0.296 0.000 0.004 0.000
#> GSM152970 2 0.4922 0.583 0.064 0.616 0.312 0.004 0.004 0.000
#> GSM152971 2 0.4152 0.611 0.032 0.664 0.304 0.000 0.000 0.000
#> GSM152972 2 0.4332 0.592 0.040 0.644 0.316 0.000 0.000 0.000
#> GSM152973 2 0.4441 0.645 0.000 0.700 0.208 0.000 0.092 0.000
#> GSM152974 2 0.1794 0.745 0.000 0.924 0.040 0.000 0.036 0.000
#> GSM152975 2 0.2959 0.743 0.008 0.844 0.124 0.000 0.024 0.000
#> GSM152976 2 0.4569 0.632 0.036 0.660 0.288 0.000 0.016 0.000
#> GSM152977 2 0.4602 0.651 0.032 0.668 0.276 0.000 0.024 0.000
#> GSM152978 2 0.4011 0.621 0.024 0.672 0.304 0.000 0.000 0.000
#> GSM152979 2 0.4719 0.611 0.004 0.680 0.216 0.000 0.100 0.000
#> GSM152980 2 0.3403 0.733 0.000 0.768 0.212 0.000 0.020 0.000
#> GSM152981 5 0.1610 0.740 0.000 0.084 0.000 0.000 0.916 0.000
#> GSM152982 2 0.4621 0.651 0.032 0.664 0.280 0.000 0.024 0.000
#> GSM152983 2 0.4493 0.608 0.036 0.644 0.312 0.000 0.008 0.000
#> GSM152984 2 0.4328 0.644 0.000 0.708 0.212 0.000 0.080 0.000
#> GSM152985 2 0.4482 0.580 0.048 0.628 0.324 0.000 0.000 0.000
#> GSM152986 2 0.4332 0.592 0.040 0.644 0.316 0.000 0.000 0.000
#> GSM152987 3 0.6989 0.000 0.220 0.008 0.404 0.328 0.032 0.008
#> GSM152988 2 0.4121 0.716 0.004 0.736 0.200 0.000 0.060 0.000
#> GSM152989 2 0.4483 0.595 0.040 0.636 0.320 0.000 0.004 0.000
#> GSM152990 2 0.4298 0.658 0.004 0.732 0.176 0.000 0.088 0.000
#> GSM152991 2 0.2740 0.731 0.000 0.864 0.076 0.000 0.060 0.000
#> GSM187524 1 0.3454 0.673 0.760 0.000 0.012 0.004 0.000 0.224
#> GSM187525 1 0.3454 0.673 0.760 0.000 0.012 0.004 0.000 0.224
#> GSM187526 1 0.3936 0.720 0.700 0.000 0.020 0.004 0.000 0.276
#> GSM187527 6 0.1003 0.899 0.028 0.000 0.004 0.004 0.000 0.964
#> GSM152856 6 0.0146 0.933 0.004 0.000 0.000 0.000 0.000 0.996
#> GSM152857 6 0.0260 0.932 0.008 0.000 0.000 0.000 0.000 0.992
#> GSM152858 1 0.3899 0.848 0.592 0.000 0.004 0.000 0.000 0.404
#> GSM152859 1 0.3262 0.462 0.820 0.000 0.020 0.004 0.008 0.148
#> GSM152860 1 0.3899 0.848 0.592 0.000 0.004 0.000 0.000 0.404
#> GSM152861 1 0.3984 0.843 0.596 0.000 0.008 0.000 0.000 0.396
#> GSM152862 1 0.3899 0.848 0.592 0.000 0.004 0.000 0.000 0.404
#> GSM152863 6 0.3918 -0.313 0.360 0.000 0.004 0.004 0.000 0.632
#> GSM152864 1 0.3944 0.832 0.568 0.000 0.004 0.000 0.000 0.428
#> GSM152865 1 0.3944 0.832 0.568 0.000 0.004 0.000 0.000 0.428
#> GSM152866 6 0.0937 0.887 0.040 0.000 0.000 0.000 0.000 0.960
#> GSM152867 1 0.3944 0.832 0.568 0.000 0.004 0.000 0.000 0.428
#> GSM152868 1 0.3944 0.832 0.568 0.000 0.004 0.000 0.000 0.428
#> GSM152869 1 0.3944 0.832 0.568 0.000 0.004 0.000 0.000 0.428
#> GSM152870 1 0.3899 0.848 0.592 0.000 0.004 0.000 0.000 0.404
#> GSM152871 1 0.3899 0.848 0.592 0.000 0.004 0.000 0.000 0.404
#> GSM152872 1 0.3899 0.848 0.592 0.000 0.004 0.000 0.000 0.404
#> GSM152873 6 0.0000 0.933 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152874 6 0.0000 0.933 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152875 6 0.0000 0.933 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152876 6 0.0260 0.932 0.008 0.000 0.000 0.000 0.000 0.992
#> GSM152877 6 0.0000 0.933 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152878 6 0.0000 0.933 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152879 6 0.0146 0.933 0.004 0.000 0.000 0.000 0.000 0.996
#> GSM152880 6 0.0146 0.933 0.004 0.000 0.000 0.000 0.000 0.996
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> CV:hclust 170 8.86e-30 2
#> CV:hclust 133 3.68e-23 3
#> CV:hclust 158 5.62e-29 4
#> CV:hclust 164 2.22e-30 5
#> CV:hclust 158 1.23e-27 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "kmeans"]
# you can also extract it by
# res = res_list["CV:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.964 0.985 0.3184 0.687 0.687
#> 3 3 0.602 0.838 0.871 0.8445 0.665 0.521
#> 4 4 0.574 0.613 0.789 0.1747 0.740 0.444
#> 5 5 0.614 0.541 0.699 0.0847 0.907 0.728
#> 6 6 0.701 0.729 0.788 0.0579 0.862 0.546
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.000 0.9877 0.000 1.000
#> GSM152805 2 0.000 0.9877 0.000 1.000
#> GSM152806 2 0.000 0.9877 0.000 1.000
#> GSM152807 2 0.000 0.9877 0.000 1.000
#> GSM152808 2 0.000 0.9877 0.000 1.000
#> GSM152809 2 0.000 0.9877 0.000 1.000
#> GSM152810 2 0.456 0.8881 0.096 0.904
#> GSM152811 2 0.000 0.9877 0.000 1.000
#> GSM152812 2 0.000 0.9877 0.000 1.000
#> GSM152813 2 0.000 0.9877 0.000 1.000
#> GSM152814 2 0.000 0.9877 0.000 1.000
#> GSM152815 2 0.000 0.9877 0.000 1.000
#> GSM152816 2 0.000 0.9877 0.000 1.000
#> GSM152817 2 0.000 0.9877 0.000 1.000
#> GSM152818 2 0.000 0.9877 0.000 1.000
#> GSM152819 2 0.000 0.9877 0.000 1.000
#> GSM152820 2 0.000 0.9877 0.000 1.000
#> GSM152821 2 0.000 0.9877 0.000 1.000
#> GSM153115 2 0.000 0.9877 0.000 1.000
#> GSM153116 2 0.000 0.9877 0.000 1.000
#> GSM153117 2 0.000 0.9877 0.000 1.000
#> GSM153118 2 0.000 0.9877 0.000 1.000
#> GSM153119 2 0.000 0.9877 0.000 1.000
#> GSM153120 2 0.714 0.7588 0.196 0.804
#> GSM153121 2 0.000 0.9877 0.000 1.000
#> GSM153122 2 0.000 0.9877 0.000 1.000
#> GSM153123 2 0.000 0.9877 0.000 1.000
#> GSM153124 2 0.000 0.9877 0.000 1.000
#> GSM153125 2 0.000 0.9877 0.000 1.000
#> GSM153126 2 0.000 0.9877 0.000 1.000
#> GSM153127 2 0.000 0.9877 0.000 1.000
#> GSM153128 2 0.000 0.9877 0.000 1.000
#> GSM153129 2 0.000 0.9877 0.000 1.000
#> GSM153130 2 0.000 0.9877 0.000 1.000
#> GSM153131 2 0.000 0.9877 0.000 1.000
#> GSM153132 2 0.000 0.9877 0.000 1.000
#> GSM153133 2 0.000 0.9877 0.000 1.000
#> GSM153134 2 0.000 0.9877 0.000 1.000
#> GSM153135 2 0.000 0.9877 0.000 1.000
#> GSM153136 2 0.000 0.9877 0.000 1.000
#> GSM153137 2 0.000 0.9877 0.000 1.000
#> GSM153138 2 0.000 0.9877 0.000 1.000
#> GSM153139 2 0.000 0.9877 0.000 1.000
#> GSM153140 2 0.000 0.9877 0.000 1.000
#> GSM153141 2 0.000 0.9877 0.000 1.000
#> GSM153142 2 0.000 0.9877 0.000 1.000
#> GSM153143 2 0.000 0.9877 0.000 1.000
#> GSM153144 2 0.000 0.9877 0.000 1.000
#> GSM153145 2 0.000 0.9877 0.000 1.000
#> GSM153146 2 0.000 0.9877 0.000 1.000
#> GSM153147 2 0.000 0.9877 0.000 1.000
#> GSM153148 2 0.000 0.9877 0.000 1.000
#> GSM153149 2 0.000 0.9877 0.000 1.000
#> GSM153150 2 0.224 0.9544 0.036 0.964
#> GSM153151 2 0.000 0.9877 0.000 1.000
#> GSM153152 2 0.000 0.9877 0.000 1.000
#> GSM153153 2 0.000 0.9877 0.000 1.000
#> GSM153154 2 0.000 0.9877 0.000 1.000
#> GSM153155 2 0.000 0.9877 0.000 1.000
#> GSM153156 2 0.000 0.9877 0.000 1.000
#> GSM153157 2 0.000 0.9877 0.000 1.000
#> GSM153158 2 0.000 0.9877 0.000 1.000
#> GSM153159 2 0.000 0.9877 0.000 1.000
#> GSM153160 2 0.000 0.9877 0.000 1.000
#> GSM153161 2 0.000 0.9877 0.000 1.000
#> GSM153162 2 0.000 0.9877 0.000 1.000
#> GSM153163 2 0.000 0.9877 0.000 1.000
#> GSM153164 2 0.000 0.9877 0.000 1.000
#> GSM153165 2 0.000 0.9877 0.000 1.000
#> GSM153166 2 0.000 0.9877 0.000 1.000
#> GSM153167 2 0.000 0.9877 0.000 1.000
#> GSM153168 2 0.000 0.9877 0.000 1.000
#> GSM153169 2 0.000 0.9877 0.000 1.000
#> GSM153170 2 0.000 0.9877 0.000 1.000
#> GSM153171 2 0.141 0.9696 0.020 0.980
#> GSM153172 2 0.000 0.9877 0.000 1.000
#> GSM153173 2 0.000 0.9877 0.000 1.000
#> GSM153174 2 0.000 0.9877 0.000 1.000
#> GSM153175 2 0.000 0.9877 0.000 1.000
#> GSM153176 2 0.000 0.9877 0.000 1.000
#> GSM153177 2 0.000 0.9877 0.000 1.000
#> GSM152931 2 0.000 0.9877 0.000 1.000
#> GSM152932 2 0.000 0.9877 0.000 1.000
#> GSM152933 2 0.000 0.9877 0.000 1.000
#> GSM152934 2 0.000 0.9877 0.000 1.000
#> GSM152935 2 0.000 0.9877 0.000 1.000
#> GSM152936 2 0.000 0.9877 0.000 1.000
#> GSM152937 2 0.000 0.9877 0.000 1.000
#> GSM152938 2 0.000 0.9877 0.000 1.000
#> GSM152939 2 0.000 0.9877 0.000 1.000
#> GSM152940 2 0.775 0.7089 0.228 0.772
#> GSM152941 1 0.000 0.9715 1.000 0.000
#> GSM152942 2 0.000 0.9877 0.000 1.000
#> GSM152943 2 0.000 0.9877 0.000 1.000
#> GSM152944 2 0.000 0.9877 0.000 1.000
#> GSM152945 2 0.000 0.9877 0.000 1.000
#> GSM152946 2 0.000 0.9877 0.000 1.000
#> GSM152947 2 0.738 0.7407 0.208 0.792
#> GSM152948 2 0.000 0.9877 0.000 1.000
#> GSM152949 2 0.000 0.9877 0.000 1.000
#> GSM152950 2 0.000 0.9877 0.000 1.000
#> GSM152951 2 0.000 0.9877 0.000 1.000
#> GSM152952 2 0.000 0.9877 0.000 1.000
#> GSM152953 2 0.000 0.9877 0.000 1.000
#> GSM152954 2 0.000 0.9877 0.000 1.000
#> GSM152955 2 0.000 0.9877 0.000 1.000
#> GSM152956 2 0.000 0.9877 0.000 1.000
#> GSM152957 2 0.430 0.8993 0.088 0.912
#> GSM152958 2 0.775 0.7091 0.228 0.772
#> GSM152959 2 0.163 0.9659 0.024 0.976
#> GSM152960 2 0.000 0.9877 0.000 1.000
#> GSM152961 2 0.775 0.7089 0.228 0.772
#> GSM152962 2 0.000 0.9877 0.000 1.000
#> GSM152963 2 0.000 0.9877 0.000 1.000
#> GSM152964 2 0.000 0.9877 0.000 1.000
#> GSM152965 2 0.000 0.9877 0.000 1.000
#> GSM152966 2 0.000 0.9877 0.000 1.000
#> GSM152967 2 0.000 0.9877 0.000 1.000
#> GSM152968 2 0.000 0.9877 0.000 1.000
#> GSM152969 2 0.000 0.9877 0.000 1.000
#> GSM152970 2 0.767 0.7155 0.224 0.776
#> GSM152971 2 0.000 0.9877 0.000 1.000
#> GSM152972 2 0.000 0.9877 0.000 1.000
#> GSM152973 2 0.000 0.9877 0.000 1.000
#> GSM152974 2 0.000 0.9877 0.000 1.000
#> GSM152975 2 0.000 0.9877 0.000 1.000
#> GSM152976 2 0.000 0.9877 0.000 1.000
#> GSM152977 2 0.000 0.9877 0.000 1.000
#> GSM152978 2 0.000 0.9877 0.000 1.000
#> GSM152979 2 0.000 0.9877 0.000 1.000
#> GSM152980 2 0.000 0.9877 0.000 1.000
#> GSM152981 2 0.000 0.9877 0.000 1.000
#> GSM152982 2 0.000 0.9877 0.000 1.000
#> GSM152983 2 0.000 0.9877 0.000 1.000
#> GSM152984 2 0.000 0.9877 0.000 1.000
#> GSM152985 1 0.969 0.3323 0.604 0.396
#> GSM152986 2 0.295 0.9382 0.052 0.948
#> GSM152987 1 0.000 0.9715 1.000 0.000
#> GSM152988 2 0.000 0.9877 0.000 1.000
#> GSM152989 1 1.000 0.0292 0.512 0.488
#> GSM152990 2 0.000 0.9877 0.000 1.000
#> GSM152991 2 0.000 0.9877 0.000 1.000
#> GSM187524 1 0.000 0.9715 1.000 0.000
#> GSM187525 1 0.000 0.9715 1.000 0.000
#> GSM187526 1 0.000 0.9715 1.000 0.000
#> GSM187527 1 0.000 0.9715 1.000 0.000
#> GSM152856 1 0.000 0.9715 1.000 0.000
#> GSM152857 1 0.000 0.9715 1.000 0.000
#> GSM152858 1 0.000 0.9715 1.000 0.000
#> GSM152859 1 0.000 0.9715 1.000 0.000
#> GSM152860 1 0.000 0.9715 1.000 0.000
#> GSM152861 1 0.000 0.9715 1.000 0.000
#> GSM152862 1 0.000 0.9715 1.000 0.000
#> GSM152863 1 0.000 0.9715 1.000 0.000
#> GSM152864 1 0.000 0.9715 1.000 0.000
#> GSM152865 1 0.000 0.9715 1.000 0.000
#> GSM152866 1 0.000 0.9715 1.000 0.000
#> GSM152867 1 0.000 0.9715 1.000 0.000
#> GSM152868 1 0.000 0.9715 1.000 0.000
#> GSM152869 1 0.000 0.9715 1.000 0.000
#> GSM152870 1 0.000 0.9715 1.000 0.000
#> GSM152871 1 0.000 0.9715 1.000 0.000
#> GSM152872 1 0.000 0.9715 1.000 0.000
#> GSM152873 1 0.000 0.9715 1.000 0.000
#> GSM152874 1 0.000 0.9715 1.000 0.000
#> GSM152875 1 0.000 0.9715 1.000 0.000
#> GSM152876 1 0.000 0.9715 1.000 0.000
#> GSM152877 1 0.000 0.9715 1.000 0.000
#> GSM152878 1 0.000 0.9715 1.000 0.000
#> GSM152879 1 0.000 0.9715 1.000 0.000
#> GSM152880 1 0.000 0.9715 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.2796 0.8906 0.000 0.908 0.092
#> GSM152805 3 0.1753 0.8044 0.000 0.048 0.952
#> GSM152806 3 0.1529 0.8026 0.000 0.040 0.960
#> GSM152807 2 0.2537 0.8965 0.000 0.920 0.080
#> GSM152808 3 0.1529 0.8026 0.000 0.040 0.960
#> GSM152809 2 0.2537 0.8965 0.000 0.920 0.080
#> GSM152810 3 0.3845 0.7345 0.012 0.116 0.872
#> GSM152811 3 0.1753 0.8080 0.000 0.048 0.952
#> GSM152812 2 0.2537 0.8965 0.000 0.920 0.080
#> GSM152813 2 0.2796 0.8906 0.000 0.908 0.092
#> GSM152814 2 0.2878 0.8877 0.000 0.904 0.096
#> GSM152815 2 0.2537 0.8965 0.000 0.920 0.080
#> GSM152816 3 0.5098 0.8180 0.000 0.248 0.752
#> GSM152817 3 0.1529 0.8026 0.000 0.040 0.960
#> GSM152818 3 0.1529 0.8026 0.000 0.040 0.960
#> GSM152819 3 0.4178 0.8316 0.000 0.172 0.828
#> GSM152820 3 0.5216 0.8097 0.000 0.260 0.740
#> GSM152821 2 0.2796 0.8906 0.000 0.908 0.092
#> GSM153115 2 0.0000 0.8888 0.000 1.000 0.000
#> GSM153116 3 0.1529 0.8026 0.000 0.040 0.960
#> GSM153117 3 0.2261 0.8145 0.000 0.068 0.932
#> GSM153118 2 0.5016 0.6797 0.000 0.760 0.240
#> GSM153119 3 0.1289 0.8002 0.000 0.032 0.968
#> GSM153120 2 0.2749 0.8292 0.064 0.924 0.012
#> GSM153121 3 0.4974 0.8246 0.000 0.236 0.764
#> GSM153122 3 0.1529 0.8065 0.000 0.040 0.960
#> GSM153123 2 0.4974 0.6928 0.000 0.764 0.236
#> GSM153124 2 0.0237 0.8902 0.000 0.996 0.004
#> GSM153125 2 0.0237 0.8902 0.000 0.996 0.004
#> GSM153126 3 0.4974 0.8246 0.000 0.236 0.764
#> GSM153127 2 0.2537 0.8965 0.000 0.920 0.080
#> GSM153128 3 0.5058 0.8137 0.000 0.244 0.756
#> GSM153129 3 0.6154 0.5564 0.000 0.408 0.592
#> GSM153130 3 0.4842 0.8286 0.000 0.224 0.776
#> GSM153131 3 0.5016 0.8219 0.000 0.240 0.760
#> GSM153132 3 0.4974 0.8246 0.000 0.236 0.764
#> GSM153133 2 0.2959 0.8869 0.000 0.900 0.100
#> GSM153134 3 0.6126 0.5750 0.000 0.400 0.600
#> GSM153135 2 0.2537 0.8965 0.000 0.920 0.080
#> GSM153136 2 0.0424 0.8872 0.000 0.992 0.008
#> GSM153137 2 0.2356 0.8974 0.000 0.928 0.072
#> GSM153138 2 0.2625 0.8967 0.000 0.916 0.084
#> GSM153139 3 0.4931 0.8264 0.000 0.232 0.768
#> GSM153140 2 0.2796 0.8906 0.000 0.908 0.092
#> GSM153141 2 0.2448 0.8972 0.000 0.924 0.076
#> GSM153142 3 0.1289 0.8002 0.000 0.032 0.968
#> GSM153143 2 0.2537 0.8965 0.000 0.920 0.080
#> GSM153144 2 0.3116 0.8807 0.000 0.892 0.108
#> GSM153145 3 0.1529 0.8026 0.000 0.040 0.960
#> GSM153146 2 0.2878 0.8877 0.000 0.904 0.096
#> GSM153147 2 0.6267 -0.0777 0.000 0.548 0.452
#> GSM153148 2 0.2537 0.8965 0.000 0.920 0.080
#> GSM153149 2 0.4002 0.8150 0.000 0.840 0.160
#> GSM153150 2 0.1015 0.8796 0.008 0.980 0.012
#> GSM153151 2 0.5291 0.6290 0.000 0.732 0.268
#> GSM153152 3 0.6291 0.3878 0.000 0.468 0.532
#> GSM153153 2 0.3482 0.8563 0.000 0.872 0.128
#> GSM153154 3 0.4555 0.8316 0.000 0.200 0.800
#> GSM153155 2 0.2796 0.8906 0.000 0.908 0.092
#> GSM153156 3 0.4974 0.8246 0.000 0.236 0.764
#> GSM153157 3 0.1529 0.8065 0.000 0.040 0.960
#> GSM153158 3 0.1643 0.8034 0.000 0.044 0.956
#> GSM153159 3 0.1289 0.8002 0.000 0.032 0.968
#> GSM153160 3 0.4931 0.8264 0.000 0.232 0.768
#> GSM153161 2 0.2448 0.8972 0.000 0.924 0.076
#> GSM153162 3 0.5905 0.6742 0.000 0.352 0.648
#> GSM153163 3 0.4931 0.8264 0.000 0.232 0.768
#> GSM153164 3 0.2796 0.8199 0.000 0.092 0.908
#> GSM153165 3 0.4974 0.8246 0.000 0.236 0.764
#> GSM153166 2 0.6299 -0.1860 0.000 0.524 0.476
#> GSM153167 2 0.4291 0.7935 0.000 0.820 0.180
#> GSM153168 3 0.1529 0.8026 0.000 0.040 0.960
#> GSM153169 3 0.4842 0.8286 0.000 0.224 0.776
#> GSM153170 3 0.5016 0.8219 0.000 0.240 0.760
#> GSM153171 2 0.0592 0.8846 0.000 0.988 0.012
#> GSM153172 2 0.2878 0.8877 0.000 0.904 0.096
#> GSM153173 3 0.4931 0.8264 0.000 0.232 0.768
#> GSM153174 2 0.3686 0.8468 0.000 0.860 0.140
#> GSM153175 2 0.0424 0.8876 0.000 0.992 0.008
#> GSM153176 2 0.6168 -0.1209 0.000 0.588 0.412
#> GSM153177 3 0.6252 0.4705 0.000 0.444 0.556
#> GSM152931 2 0.0000 0.8888 0.000 1.000 0.000
#> GSM152932 2 0.2878 0.8881 0.000 0.904 0.096
#> GSM152933 3 0.6302 0.3537 0.000 0.480 0.520
#> GSM152934 2 0.0747 0.8905 0.000 0.984 0.016
#> GSM152935 3 0.1964 0.8111 0.000 0.056 0.944
#> GSM152936 2 0.0424 0.8872 0.000 0.992 0.008
#> GSM152937 3 0.5216 0.7996 0.000 0.260 0.740
#> GSM152938 3 0.5465 0.7760 0.000 0.288 0.712
#> GSM152939 2 0.0747 0.8906 0.000 0.984 0.016
#> GSM152940 2 0.2939 0.8204 0.072 0.916 0.012
#> GSM152941 1 0.2866 0.9323 0.916 0.076 0.008
#> GSM152942 3 0.6008 0.6654 0.000 0.372 0.628
#> GSM152943 2 0.1289 0.8940 0.000 0.968 0.032
#> GSM152944 3 0.4750 0.8302 0.000 0.216 0.784
#> GSM152945 3 0.5948 0.3995 0.000 0.360 0.640
#> GSM152946 2 0.2356 0.8977 0.000 0.928 0.072
#> GSM152947 2 0.2749 0.8304 0.064 0.924 0.012
#> GSM152948 2 0.2537 0.8965 0.000 0.920 0.080
#> GSM152949 3 0.5497 0.7664 0.000 0.292 0.708
#> GSM152950 3 0.5835 0.6991 0.000 0.340 0.660
#> GSM152951 2 0.2537 0.8965 0.000 0.920 0.080
#> GSM152952 2 0.2625 0.8966 0.000 0.916 0.084
#> GSM152953 2 0.2537 0.8965 0.000 0.920 0.080
#> GSM152954 2 0.0424 0.8872 0.000 0.992 0.008
#> GSM152955 3 0.2261 0.8029 0.000 0.068 0.932
#> GSM152956 2 0.2537 0.8965 0.000 0.920 0.080
#> GSM152957 2 0.0661 0.8852 0.004 0.988 0.008
#> GSM152958 2 0.2845 0.8248 0.068 0.920 0.012
#> GSM152959 2 0.0829 0.8817 0.004 0.984 0.012
#> GSM152960 2 0.0424 0.8872 0.000 0.992 0.008
#> GSM152961 2 0.2749 0.8290 0.064 0.924 0.012
#> GSM152962 3 0.5254 0.7967 0.000 0.264 0.736
#> GSM152963 2 0.2625 0.8966 0.000 0.916 0.084
#> GSM152964 3 0.2625 0.7776 0.000 0.084 0.916
#> GSM152965 2 0.2796 0.8952 0.000 0.908 0.092
#> GSM152966 2 0.0000 0.8888 0.000 1.000 0.000
#> GSM152967 2 0.2625 0.8948 0.000 0.916 0.084
#> GSM152968 3 0.5098 0.8156 0.000 0.248 0.752
#> GSM152969 2 0.0000 0.8888 0.000 1.000 0.000
#> GSM152970 2 0.2939 0.8218 0.072 0.916 0.012
#> GSM152971 2 0.0424 0.8872 0.000 0.992 0.008
#> GSM152972 2 0.0424 0.8872 0.000 0.992 0.008
#> GSM152973 2 0.1860 0.8798 0.000 0.948 0.052
#> GSM152974 2 0.2878 0.8877 0.000 0.904 0.096
#> GSM152975 2 0.2711 0.8950 0.000 0.912 0.088
#> GSM152976 2 0.0424 0.8872 0.000 0.992 0.008
#> GSM152977 2 0.0424 0.8872 0.000 0.992 0.008
#> GSM152978 2 0.0424 0.8872 0.000 0.992 0.008
#> GSM152979 3 0.4121 0.8316 0.000 0.168 0.832
#> GSM152980 2 0.2796 0.8906 0.000 0.908 0.092
#> GSM152981 3 0.1529 0.8026 0.000 0.040 0.960
#> GSM152982 2 0.0592 0.8889 0.000 0.988 0.012
#> GSM152983 2 0.0424 0.8872 0.000 0.992 0.008
#> GSM152984 2 0.4346 0.7871 0.000 0.816 0.184
#> GSM152985 2 0.3769 0.7777 0.104 0.880 0.016
#> GSM152986 2 0.0237 0.8882 0.000 0.996 0.004
#> GSM152987 1 0.2955 0.9272 0.912 0.080 0.008
#> GSM152988 2 0.0892 0.8910 0.000 0.980 0.020
#> GSM152989 2 0.3207 0.8078 0.084 0.904 0.012
#> GSM152990 3 0.4974 0.8246 0.000 0.236 0.764
#> GSM152991 3 0.4062 0.8308 0.000 0.164 0.836
#> GSM187524 1 0.1015 0.9823 0.980 0.012 0.008
#> GSM187525 1 0.1015 0.9823 0.980 0.012 0.008
#> GSM187526 1 0.1015 0.9823 0.980 0.012 0.008
#> GSM187527 1 0.0892 0.9830 0.980 0.000 0.020
#> GSM152856 1 0.0892 0.9830 0.980 0.000 0.020
#> GSM152857 1 0.0892 0.9830 0.980 0.000 0.020
#> GSM152858 1 0.1182 0.9820 0.976 0.012 0.012
#> GSM152859 1 0.1182 0.9820 0.976 0.012 0.012
#> GSM152860 1 0.1182 0.9820 0.976 0.012 0.012
#> GSM152861 1 0.0237 0.9846 0.996 0.004 0.000
#> GSM152862 1 0.1182 0.9820 0.976 0.012 0.012
#> GSM152863 1 0.0000 0.9841 1.000 0.000 0.000
#> GSM152864 1 0.0237 0.9846 0.996 0.004 0.000
#> GSM152865 1 0.0237 0.9846 0.996 0.004 0.000
#> GSM152866 1 0.0892 0.9830 0.980 0.000 0.020
#> GSM152867 1 0.0237 0.9846 0.996 0.004 0.000
#> GSM152868 1 0.0237 0.9846 0.996 0.004 0.000
#> GSM152869 1 0.0237 0.9846 0.996 0.004 0.000
#> GSM152870 1 0.1182 0.9820 0.976 0.012 0.012
#> GSM152871 1 0.1182 0.9820 0.976 0.012 0.012
#> GSM152872 1 0.1182 0.9820 0.976 0.012 0.012
#> GSM152873 1 0.0892 0.9830 0.980 0.000 0.020
#> GSM152874 1 0.0892 0.9830 0.980 0.000 0.020
#> GSM152875 1 0.0892 0.9830 0.980 0.000 0.020
#> GSM152876 1 0.0892 0.9830 0.980 0.000 0.020
#> GSM152877 1 0.0892 0.9830 0.980 0.000 0.020
#> GSM152878 1 0.0892 0.9830 0.980 0.000 0.020
#> GSM152879 1 0.0892 0.9830 0.980 0.000 0.020
#> GSM152880 1 0.0892 0.9830 0.980 0.000 0.020
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.4188 0.5853 0.000 0.752 0.004 0.244
#> GSM152805 3 0.4277 0.8902 0.000 0.280 0.720 0.000
#> GSM152806 3 0.4193 0.8994 0.000 0.268 0.732 0.000
#> GSM152807 2 0.5168 0.0741 0.000 0.504 0.004 0.492
#> GSM152808 3 0.4193 0.8994 0.000 0.268 0.732 0.000
#> GSM152809 2 0.5168 0.0741 0.000 0.504 0.004 0.492
#> GSM152810 3 0.4534 0.6752 0.000 0.068 0.800 0.132
#> GSM152811 3 0.4746 0.8673 0.000 0.304 0.688 0.008
#> GSM152812 2 0.5167 0.0878 0.000 0.508 0.004 0.488
#> GSM152813 2 0.3942 0.5965 0.000 0.764 0.000 0.236
#> GSM152814 2 0.4088 0.6003 0.000 0.764 0.004 0.232
#> GSM152815 2 0.5167 0.0878 0.000 0.508 0.004 0.488
#> GSM152816 2 0.2589 0.5452 0.000 0.884 0.116 0.000
#> GSM152817 3 0.4193 0.8994 0.000 0.268 0.732 0.000
#> GSM152818 3 0.4193 0.8994 0.000 0.268 0.732 0.000
#> GSM152819 2 0.3088 0.5397 0.000 0.864 0.128 0.008
#> GSM152820 2 0.2149 0.5699 0.000 0.912 0.088 0.000
#> GSM152821 2 0.4608 0.5128 0.000 0.692 0.004 0.304
#> GSM153115 4 0.1474 0.8103 0.000 0.052 0.000 0.948
#> GSM153116 3 0.4193 0.8994 0.000 0.268 0.732 0.000
#> GSM153117 2 0.4500 0.0703 0.000 0.684 0.316 0.000
#> GSM153118 2 0.3583 0.6419 0.000 0.816 0.004 0.180
#> GSM153119 3 0.3444 0.8556 0.000 0.184 0.816 0.000
#> GSM153120 4 0.2542 0.7688 0.000 0.012 0.084 0.904
#> GSM153121 2 0.3074 0.5013 0.000 0.848 0.152 0.000
#> GSM153122 3 0.4018 0.8490 0.000 0.224 0.772 0.004
#> GSM153123 2 0.3311 0.6435 0.000 0.828 0.000 0.172
#> GSM153124 4 0.1716 0.8040 0.000 0.064 0.000 0.936
#> GSM153125 4 0.1474 0.8103 0.000 0.052 0.000 0.948
#> GSM153126 2 0.3123 0.4959 0.000 0.844 0.156 0.000
#> GSM153127 2 0.5168 0.0594 0.000 0.500 0.004 0.496
#> GSM153128 2 0.6642 -0.2237 0.000 0.492 0.424 0.084
#> GSM153129 2 0.1302 0.6426 0.000 0.956 0.000 0.044
#> GSM153130 2 0.3172 0.4900 0.000 0.840 0.160 0.000
#> GSM153131 2 0.2281 0.5602 0.000 0.904 0.096 0.000
#> GSM153132 2 0.2149 0.5693 0.000 0.912 0.088 0.000
#> GSM153133 2 0.3837 0.6069 0.000 0.776 0.000 0.224
#> GSM153134 2 0.1302 0.6433 0.000 0.956 0.000 0.044
#> GSM153135 2 0.5168 0.0741 0.000 0.504 0.004 0.492
#> GSM153136 4 0.1118 0.8167 0.000 0.036 0.000 0.964
#> GSM153137 4 0.5157 0.4953 0.000 0.284 0.028 0.688
#> GSM153138 4 0.5865 0.3471 0.000 0.340 0.048 0.612
#> GSM153139 2 0.3123 0.4959 0.000 0.844 0.156 0.000
#> GSM153140 2 0.4655 0.4945 0.000 0.684 0.004 0.312
#> GSM153141 4 0.5408 -0.0576 0.000 0.488 0.012 0.500
#> GSM153142 3 0.4193 0.8994 0.000 0.268 0.732 0.000
#> GSM153143 4 0.5168 -0.0772 0.000 0.496 0.004 0.500
#> GSM153144 2 0.3801 0.6074 0.000 0.780 0.000 0.220
#> GSM153145 3 0.4193 0.8994 0.000 0.268 0.732 0.000
#> GSM153146 2 0.4584 0.5191 0.000 0.696 0.004 0.300
#> GSM153147 2 0.2831 0.6638 0.000 0.876 0.004 0.120
#> GSM153148 2 0.5168 0.0741 0.000 0.504 0.004 0.492
#> GSM153149 2 0.3688 0.6212 0.000 0.792 0.000 0.208
#> GSM153150 4 0.2593 0.7699 0.000 0.016 0.080 0.904
#> GSM153151 2 0.6595 0.4699 0.000 0.604 0.120 0.276
#> GSM153152 2 0.2589 0.6632 0.000 0.884 0.000 0.116
#> GSM153153 2 0.3908 0.6191 0.000 0.784 0.004 0.212
#> GSM153154 2 0.2760 0.5283 0.000 0.872 0.128 0.000
#> GSM153155 2 0.4679 0.4323 0.000 0.648 0.000 0.352
#> GSM153156 2 0.3074 0.5013 0.000 0.848 0.152 0.000
#> GSM153157 3 0.4356 0.8815 0.000 0.292 0.708 0.000
#> GSM153158 2 0.4877 -0.2261 0.000 0.592 0.408 0.000
#> GSM153159 3 0.4193 0.8994 0.000 0.268 0.732 0.000
#> GSM153160 2 0.3172 0.4900 0.000 0.840 0.160 0.000
#> GSM153161 4 0.5404 -0.0118 0.000 0.476 0.012 0.512
#> GSM153162 2 0.0779 0.6274 0.000 0.980 0.004 0.016
#> GSM153163 2 0.3123 0.4959 0.000 0.844 0.156 0.000
#> GSM153164 2 0.4522 0.0607 0.000 0.680 0.320 0.000
#> GSM153165 2 0.2647 0.5377 0.000 0.880 0.120 0.000
#> GSM153166 2 0.2197 0.6559 0.000 0.916 0.004 0.080
#> GSM153167 2 0.3444 0.6355 0.000 0.816 0.000 0.184
#> GSM153168 3 0.4193 0.8994 0.000 0.268 0.732 0.000
#> GSM153169 2 0.3172 0.4900 0.000 0.840 0.160 0.000
#> GSM153170 2 0.1557 0.5892 0.000 0.944 0.056 0.000
#> GSM153171 4 0.0592 0.8152 0.000 0.016 0.000 0.984
#> GSM153172 2 0.3907 0.6010 0.000 0.768 0.000 0.232
#> GSM153173 2 0.3074 0.5015 0.000 0.848 0.152 0.000
#> GSM153174 2 0.3649 0.6216 0.000 0.796 0.000 0.204
#> GSM153175 4 0.1211 0.8159 0.000 0.040 0.000 0.960
#> GSM153176 4 0.4502 0.5550 0.000 0.236 0.016 0.748
#> GSM153177 2 0.2125 0.6531 0.000 0.920 0.004 0.076
#> GSM152931 4 0.1637 0.8055 0.000 0.060 0.000 0.940
#> GSM152932 2 0.4155 0.5887 0.000 0.756 0.004 0.240
#> GSM152933 2 0.1978 0.6505 0.000 0.928 0.004 0.068
#> GSM152934 4 0.3176 0.7691 0.000 0.036 0.084 0.880
#> GSM152935 3 0.5793 0.5870 0.000 0.384 0.580 0.036
#> GSM152936 4 0.1174 0.8139 0.000 0.020 0.012 0.968
#> GSM152937 2 0.7554 -0.2521 0.000 0.432 0.376 0.192
#> GSM152938 2 0.5548 0.4540 0.000 0.716 0.200 0.084
#> GSM152939 4 0.3311 0.7095 0.000 0.172 0.000 0.828
#> GSM152940 4 0.2665 0.7613 0.004 0.008 0.088 0.900
#> GSM152941 1 0.6926 0.3133 0.460 0.000 0.108 0.432
#> GSM152942 2 0.3761 0.5712 0.000 0.852 0.080 0.068
#> GSM152943 4 0.4093 0.7479 0.000 0.072 0.096 0.832
#> GSM152944 2 0.3123 0.4933 0.000 0.844 0.156 0.000
#> GSM152945 3 0.6220 0.5978 0.000 0.104 0.648 0.248
#> GSM152946 4 0.5165 -0.0107 0.000 0.484 0.004 0.512
#> GSM152947 4 0.2727 0.7676 0.004 0.012 0.084 0.900
#> GSM152948 2 0.5167 0.0873 0.000 0.508 0.004 0.488
#> GSM152949 2 0.1174 0.6183 0.000 0.968 0.020 0.012
#> GSM152950 2 0.1411 0.6231 0.000 0.960 0.020 0.020
#> GSM152951 2 0.4998 0.0898 0.000 0.512 0.000 0.488
#> GSM152952 4 0.5404 -0.0118 0.000 0.476 0.012 0.512
#> GSM152953 2 0.5409 0.0544 0.000 0.496 0.012 0.492
#> GSM152954 4 0.0707 0.8160 0.000 0.020 0.000 0.980
#> GSM152955 3 0.6513 0.7164 0.000 0.176 0.640 0.184
#> GSM152956 2 0.5155 0.1484 0.000 0.528 0.004 0.468
#> GSM152957 4 0.0592 0.8152 0.000 0.016 0.000 0.984
#> GSM152958 4 0.0779 0.8152 0.004 0.016 0.000 0.980
#> GSM152959 4 0.0927 0.8124 0.000 0.016 0.008 0.976
#> GSM152960 4 0.1059 0.8145 0.000 0.016 0.012 0.972
#> GSM152961 4 0.0592 0.8152 0.000 0.016 0.000 0.984
#> GSM152962 2 0.4050 0.5460 0.000 0.808 0.168 0.024
#> GSM152963 4 0.5408 -0.0576 0.000 0.488 0.012 0.500
#> GSM152964 3 0.4944 0.8034 0.000 0.160 0.768 0.072
#> GSM152965 2 0.6347 0.1673 0.000 0.524 0.064 0.412
#> GSM152966 4 0.1637 0.8055 0.000 0.060 0.000 0.940
#> GSM152967 2 0.4193 0.5620 0.000 0.732 0.000 0.268
#> GSM152968 2 0.1118 0.6006 0.000 0.964 0.036 0.000
#> GSM152969 4 0.1118 0.8167 0.000 0.036 0.000 0.964
#> GSM152970 4 0.1771 0.7955 0.004 0.012 0.036 0.948
#> GSM152971 4 0.1118 0.8167 0.000 0.036 0.000 0.964
#> GSM152972 4 0.1118 0.8167 0.000 0.036 0.000 0.964
#> GSM152973 2 0.4985 0.1633 0.000 0.532 0.000 0.468
#> GSM152974 2 0.3907 0.6010 0.000 0.768 0.000 0.232
#> GSM152975 4 0.4837 0.3838 0.000 0.348 0.004 0.648
#> GSM152976 4 0.1022 0.8172 0.000 0.032 0.000 0.968
#> GSM152977 4 0.0921 0.8169 0.000 0.028 0.000 0.972
#> GSM152978 4 0.0707 0.8167 0.000 0.020 0.000 0.980
#> GSM152979 2 0.3356 0.4581 0.000 0.824 0.176 0.000
#> GSM152980 4 0.4872 0.3415 0.000 0.356 0.004 0.640
#> GSM152981 3 0.4164 0.8981 0.000 0.264 0.736 0.000
#> GSM152982 4 0.1211 0.8159 0.000 0.040 0.000 0.960
#> GSM152983 4 0.1211 0.8159 0.000 0.040 0.000 0.960
#> GSM152984 2 0.3908 0.6268 0.000 0.784 0.004 0.212
#> GSM152985 4 0.2727 0.7493 0.012 0.004 0.084 0.900
#> GSM152986 4 0.1022 0.8166 0.000 0.032 0.000 0.968
#> GSM152987 1 0.7512 0.3831 0.460 0.000 0.192 0.348
#> GSM152988 4 0.4977 0.0517 0.000 0.460 0.000 0.540
#> GSM152989 4 0.0657 0.8140 0.004 0.012 0.000 0.984
#> GSM152990 2 0.3024 0.5064 0.000 0.852 0.148 0.000
#> GSM152991 2 0.4936 0.1325 0.000 0.652 0.340 0.008
#> GSM187524 1 0.2988 0.8866 0.876 0.000 0.112 0.012
#> GSM187525 1 0.2988 0.8866 0.876 0.000 0.112 0.012
#> GSM187526 1 0.2988 0.8866 0.876 0.000 0.112 0.012
#> GSM187527 1 0.2124 0.9089 0.924 0.000 0.068 0.008
#> GSM152856 1 0.2124 0.9089 0.924 0.000 0.068 0.008
#> GSM152857 1 0.2124 0.9089 0.924 0.000 0.068 0.008
#> GSM152858 1 0.2342 0.8997 0.912 0.000 0.080 0.008
#> GSM152859 1 0.3047 0.8849 0.872 0.000 0.116 0.012
#> GSM152860 1 0.2342 0.8997 0.912 0.000 0.080 0.008
#> GSM152861 1 0.0779 0.9125 0.980 0.000 0.016 0.004
#> GSM152862 1 0.2342 0.8997 0.912 0.000 0.080 0.008
#> GSM152863 1 0.0188 0.9146 0.996 0.000 0.004 0.000
#> GSM152864 1 0.0000 0.9143 1.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.9143 1.000 0.000 0.000 0.000
#> GSM152866 1 0.2480 0.9090 0.904 0.000 0.088 0.008
#> GSM152867 1 0.0188 0.9146 0.996 0.000 0.000 0.004
#> GSM152868 1 0.0188 0.9146 0.996 0.000 0.000 0.004
#> GSM152869 1 0.0188 0.9146 0.996 0.000 0.000 0.004
#> GSM152870 1 0.2342 0.8997 0.912 0.000 0.080 0.008
#> GSM152871 1 0.2342 0.8997 0.912 0.000 0.080 0.008
#> GSM152872 1 0.2342 0.8997 0.912 0.000 0.080 0.008
#> GSM152873 1 0.2255 0.9088 0.920 0.000 0.068 0.012
#> GSM152874 1 0.2255 0.9088 0.920 0.000 0.068 0.012
#> GSM152875 1 0.2255 0.9088 0.920 0.000 0.068 0.012
#> GSM152876 1 0.2124 0.9089 0.924 0.000 0.068 0.008
#> GSM152877 1 0.2255 0.9088 0.920 0.000 0.068 0.012
#> GSM152878 1 0.2255 0.9088 0.920 0.000 0.068 0.012
#> GSM152879 1 0.2124 0.9089 0.924 0.000 0.068 0.008
#> GSM152880 1 0.2124 0.9089 0.924 0.000 0.068 0.008
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.5961 0.4172 0.000 0.580 0.260 0.160 0.000
#> GSM152805 5 0.1121 0.7704 0.000 0.044 0.000 0.000 0.956
#> GSM152806 5 0.1043 0.7721 0.000 0.040 0.000 0.000 0.960
#> GSM152807 2 0.6744 0.2010 0.000 0.404 0.272 0.324 0.000
#> GSM152808 5 0.1043 0.7721 0.000 0.040 0.000 0.000 0.960
#> GSM152809 2 0.6744 0.2010 0.000 0.404 0.272 0.324 0.000
#> GSM152810 5 0.5569 0.4534 0.000 0.000 0.320 0.092 0.588
#> GSM152811 5 0.2597 0.7276 0.000 0.092 0.000 0.024 0.884
#> GSM152812 2 0.6744 0.2010 0.000 0.404 0.272 0.324 0.000
#> GSM152813 2 0.5427 0.4613 0.000 0.636 0.260 0.104 0.000
#> GSM152814 2 0.5404 0.4611 0.000 0.636 0.264 0.100 0.000
#> GSM152815 2 0.6744 0.2010 0.000 0.404 0.272 0.324 0.000
#> GSM152816 2 0.3963 0.4934 0.000 0.808 0.084 0.004 0.104
#> GSM152817 5 0.1043 0.7721 0.000 0.040 0.000 0.000 0.960
#> GSM152818 5 0.1043 0.7721 0.000 0.040 0.000 0.000 0.960
#> GSM152819 2 0.6048 0.4343 0.000 0.588 0.248 0.004 0.160
#> GSM152820 2 0.5812 0.4807 0.000 0.656 0.228 0.036 0.080
#> GSM152821 2 0.5987 0.4095 0.000 0.572 0.272 0.156 0.000
#> GSM153115 4 0.0912 0.8399 0.000 0.016 0.012 0.972 0.000
#> GSM153116 5 0.1671 0.7472 0.000 0.076 0.000 0.000 0.924
#> GSM153117 5 0.6032 -0.0578 0.000 0.424 0.116 0.000 0.460
#> GSM153118 2 0.5309 0.4647 0.000 0.644 0.264 0.092 0.000
#> GSM153119 5 0.4275 0.5877 0.000 0.020 0.284 0.000 0.696
#> GSM153120 4 0.4574 0.5074 0.008 0.012 0.328 0.652 0.000
#> GSM153121 2 0.2741 0.4599 0.000 0.860 0.004 0.004 0.132
#> GSM153122 5 0.6006 0.4055 0.000 0.124 0.356 0.000 0.520
#> GSM153123 2 0.2735 0.5086 0.000 0.880 0.084 0.036 0.000
#> GSM153124 4 0.1012 0.8383 0.000 0.020 0.012 0.968 0.000
#> GSM153125 4 0.0912 0.8399 0.000 0.016 0.012 0.972 0.000
#> GSM153126 2 0.2921 0.4461 0.000 0.844 0.004 0.004 0.148
#> GSM153127 2 0.6754 0.1946 0.000 0.400 0.276 0.324 0.000
#> GSM153128 3 0.7328 0.0794 0.000 0.300 0.424 0.032 0.244
#> GSM153129 2 0.0807 0.5109 0.000 0.976 0.000 0.012 0.012
#> GSM153130 2 0.2806 0.4431 0.000 0.844 0.000 0.004 0.152
#> GSM153131 2 0.2179 0.4814 0.000 0.896 0.000 0.004 0.100
#> GSM153132 2 0.2974 0.5033 0.000 0.868 0.052 0.000 0.080
#> GSM153133 2 0.5088 0.4792 0.000 0.680 0.228 0.092 0.000
#> GSM153134 2 0.0807 0.5125 0.000 0.976 0.012 0.012 0.000
#> GSM153135 2 0.6754 0.1946 0.000 0.400 0.276 0.324 0.000
#> GSM153136 4 0.0912 0.8399 0.000 0.016 0.012 0.972 0.000
#> GSM153137 3 0.6612 0.1543 0.000 0.216 0.412 0.372 0.000
#> GSM153138 3 0.6533 0.2173 0.000 0.224 0.472 0.304 0.000
#> GSM153139 2 0.2719 0.4514 0.000 0.852 0.000 0.004 0.144
#> GSM153140 2 0.6268 0.3684 0.000 0.536 0.260 0.204 0.000
#> GSM153141 2 0.6798 0.1465 0.000 0.376 0.300 0.324 0.000
#> GSM153142 5 0.1043 0.7721 0.000 0.040 0.000 0.000 0.960
#> GSM153143 2 0.6754 0.1854 0.000 0.396 0.272 0.332 0.000
#> GSM153144 2 0.3237 0.5069 0.000 0.848 0.104 0.048 0.000
#> GSM153145 5 0.1043 0.7721 0.000 0.040 0.000 0.000 0.960
#> GSM153146 2 0.5920 0.4175 0.000 0.580 0.272 0.148 0.000
#> GSM153147 2 0.1653 0.5081 0.000 0.944 0.004 0.028 0.024
#> GSM153148 2 0.6754 0.1946 0.000 0.400 0.276 0.324 0.000
#> GSM153149 2 0.5232 0.4668 0.000 0.648 0.268 0.084 0.000
#> GSM153150 4 0.3280 0.7045 0.000 0.012 0.176 0.812 0.000
#> GSM153151 2 0.6577 -0.2262 0.000 0.460 0.408 0.104 0.028
#> GSM153152 2 0.1117 0.5116 0.000 0.964 0.016 0.020 0.000
#> GSM153153 2 0.5309 0.4647 0.000 0.644 0.264 0.092 0.000
#> GSM153154 2 0.2389 0.4727 0.000 0.880 0.000 0.004 0.116
#> GSM153155 2 0.6244 0.3706 0.000 0.540 0.260 0.200 0.000
#> GSM153156 2 0.2787 0.4568 0.000 0.856 0.004 0.004 0.136
#> GSM153157 5 0.2286 0.7248 0.000 0.108 0.004 0.000 0.888
#> GSM153158 5 0.4650 0.1331 0.000 0.468 0.012 0.000 0.520
#> GSM153159 5 0.1121 0.7706 0.000 0.044 0.000 0.000 0.956
#> GSM153160 2 0.2964 0.4417 0.000 0.840 0.004 0.004 0.152
#> GSM153161 2 0.6821 0.0821 0.000 0.352 0.324 0.324 0.000
#> GSM153162 2 0.1569 0.5026 0.000 0.944 0.004 0.008 0.044
#> GSM153163 2 0.2719 0.4514 0.000 0.852 0.000 0.004 0.144
#> GSM153164 2 0.6219 0.1155 0.000 0.440 0.140 0.000 0.420
#> GSM153165 2 0.2439 0.4701 0.000 0.876 0.000 0.004 0.120
#> GSM153166 2 0.4054 0.4871 0.000 0.732 0.248 0.020 0.000
#> GSM153167 2 0.1997 0.5143 0.000 0.924 0.040 0.036 0.000
#> GSM153168 5 0.1043 0.7721 0.000 0.040 0.000 0.000 0.960
#> GSM153169 2 0.2806 0.4431 0.000 0.844 0.000 0.004 0.152
#> GSM153170 2 0.1892 0.4906 0.000 0.916 0.000 0.004 0.080
#> GSM153171 4 0.0912 0.8400 0.000 0.012 0.016 0.972 0.000
#> GSM153172 2 0.5404 0.4611 0.000 0.636 0.264 0.100 0.000
#> GSM153173 2 0.2629 0.4584 0.000 0.860 0.000 0.004 0.136
#> GSM153174 2 0.1124 0.5083 0.000 0.960 0.004 0.036 0.000
#> GSM153175 4 0.1697 0.8139 0.000 0.060 0.008 0.932 0.000
#> GSM153176 4 0.3630 0.5842 0.000 0.204 0.016 0.780 0.000
#> GSM153177 2 0.4640 0.4789 0.000 0.696 0.256 0.048 0.000
#> GSM152931 4 0.0912 0.8399 0.000 0.016 0.012 0.972 0.000
#> GSM152932 2 0.5400 0.4588 0.000 0.632 0.272 0.096 0.000
#> GSM152933 2 0.4830 0.4749 0.000 0.684 0.256 0.060 0.000
#> GSM152934 4 0.4585 0.4615 0.000 0.020 0.352 0.628 0.000
#> GSM152935 3 0.6836 -0.2256 0.000 0.188 0.404 0.012 0.396
#> GSM152936 4 0.1281 0.8334 0.000 0.012 0.032 0.956 0.000
#> GSM152937 3 0.7603 0.1197 0.000 0.340 0.412 0.068 0.180
#> GSM152938 2 0.6040 -0.1336 0.000 0.540 0.372 0.032 0.056
#> GSM152939 4 0.3720 0.5801 0.000 0.228 0.012 0.760 0.000
#> GSM152940 4 0.4190 0.6066 0.008 0.012 0.256 0.724 0.000
#> GSM152941 4 0.7102 0.0165 0.328 0.000 0.208 0.440 0.024
#> GSM152942 2 0.2952 0.4768 0.000 0.872 0.004 0.036 0.088
#> GSM152943 4 0.5393 0.2262 0.000 0.056 0.440 0.504 0.000
#> GSM152944 2 0.2674 0.4549 0.000 0.856 0.000 0.004 0.140
#> GSM152945 5 0.6096 0.2995 0.000 0.004 0.412 0.108 0.476
#> GSM152946 2 0.6759 0.1772 0.000 0.396 0.276 0.328 0.000
#> GSM152947 4 0.4190 0.6077 0.008 0.012 0.256 0.724 0.000
#> GSM152948 2 0.6744 0.2010 0.000 0.404 0.272 0.324 0.000
#> GSM152949 2 0.1717 0.5005 0.000 0.936 0.004 0.008 0.052
#> GSM152950 2 0.1725 0.5039 0.000 0.936 0.020 0.000 0.044
#> GSM152951 2 0.6744 0.2010 0.000 0.404 0.272 0.324 0.000
#> GSM152952 2 0.6819 0.0932 0.000 0.356 0.320 0.324 0.000
#> GSM152953 2 0.6810 0.1228 0.000 0.368 0.316 0.316 0.000
#> GSM152954 4 0.0912 0.8429 0.000 0.012 0.016 0.972 0.000
#> GSM152955 5 0.6160 0.4211 0.000 0.012 0.284 0.128 0.576
#> GSM152956 2 0.6744 0.2010 0.000 0.404 0.272 0.324 0.000
#> GSM152957 4 0.0693 0.8421 0.000 0.012 0.008 0.980 0.000
#> GSM152958 4 0.0854 0.8418 0.008 0.012 0.004 0.976 0.000
#> GSM152959 4 0.1195 0.8335 0.000 0.012 0.028 0.960 0.000
#> GSM152960 4 0.1549 0.8319 0.000 0.016 0.040 0.944 0.000
#> GSM152961 4 0.1095 0.8388 0.008 0.012 0.012 0.968 0.000
#> GSM152962 2 0.5636 -0.0729 0.000 0.560 0.372 0.012 0.056
#> GSM152963 2 0.6813 0.1134 0.000 0.364 0.320 0.316 0.000
#> GSM152964 5 0.5277 0.4262 0.000 0.012 0.416 0.028 0.544
#> GSM152965 3 0.6416 0.0893 0.000 0.292 0.500 0.208 0.000
#> GSM152966 4 0.0912 0.8399 0.000 0.016 0.012 0.972 0.000
#> GSM152967 2 0.5738 0.4394 0.000 0.604 0.264 0.132 0.000
#> GSM152968 2 0.1571 0.4979 0.000 0.936 0.000 0.004 0.060
#> GSM152969 4 0.0912 0.8408 0.000 0.012 0.016 0.972 0.000
#> GSM152970 4 0.2354 0.7948 0.008 0.012 0.076 0.904 0.000
#> GSM152971 4 0.0912 0.8399 0.000 0.016 0.012 0.972 0.000
#> GSM152972 4 0.0912 0.8399 0.000 0.016 0.012 0.972 0.000
#> GSM152973 2 0.3990 0.1973 0.000 0.688 0.004 0.308 0.000
#> GSM152974 2 0.5404 0.4611 0.000 0.636 0.264 0.100 0.000
#> GSM152975 4 0.5899 0.0731 0.000 0.248 0.160 0.592 0.000
#> GSM152976 4 0.0566 0.8429 0.000 0.012 0.004 0.984 0.000
#> GSM152977 4 0.0693 0.8430 0.000 0.012 0.008 0.980 0.000
#> GSM152978 4 0.0912 0.8420 0.000 0.016 0.012 0.972 0.000
#> GSM152979 2 0.2763 0.4477 0.000 0.848 0.000 0.004 0.148
#> GSM152980 4 0.6057 0.0156 0.000 0.224 0.200 0.576 0.000
#> GSM152981 5 0.1043 0.7721 0.000 0.040 0.000 0.000 0.960
#> GSM152982 4 0.0703 0.8413 0.000 0.024 0.000 0.976 0.000
#> GSM152983 4 0.0798 0.8413 0.000 0.016 0.008 0.976 0.000
#> GSM152984 2 0.2520 0.4814 0.000 0.888 0.004 0.096 0.012
#> GSM152985 4 0.1644 0.8268 0.008 0.012 0.028 0.948 0.004
#> GSM152986 4 0.0798 0.8409 0.000 0.016 0.008 0.976 0.000
#> GSM152987 3 0.6310 0.0479 0.184 0.000 0.580 0.224 0.012
#> GSM152988 2 0.4590 0.0555 0.000 0.568 0.012 0.420 0.000
#> GSM152989 4 0.1299 0.8352 0.008 0.012 0.020 0.960 0.000
#> GSM152990 2 0.2646 0.4660 0.000 0.868 0.004 0.004 0.124
#> GSM152991 2 0.7023 0.1666 0.000 0.444 0.240 0.016 0.300
#> GSM187524 1 0.4453 0.8018 0.744 0.000 0.212 0.020 0.024
#> GSM187525 1 0.4421 0.8048 0.748 0.000 0.208 0.020 0.024
#> GSM187526 1 0.4356 0.8106 0.756 0.000 0.200 0.020 0.024
#> GSM187527 1 0.2583 0.8816 0.864 0.000 0.132 0.000 0.004
#> GSM152856 1 0.2583 0.8816 0.864 0.000 0.132 0.000 0.004
#> GSM152857 1 0.2583 0.8816 0.864 0.000 0.132 0.000 0.004
#> GSM152858 1 0.3314 0.8587 0.852 0.000 0.108 0.020 0.020
#> GSM152859 1 0.4380 0.8099 0.752 0.000 0.204 0.016 0.028
#> GSM152860 1 0.3314 0.8587 0.852 0.000 0.108 0.020 0.020
#> GSM152861 1 0.0854 0.8895 0.976 0.000 0.012 0.004 0.008
#> GSM152862 1 0.3314 0.8587 0.852 0.000 0.108 0.020 0.020
#> GSM152863 1 0.0566 0.8917 0.984 0.000 0.012 0.000 0.004
#> GSM152864 1 0.0324 0.8915 0.992 0.000 0.000 0.004 0.004
#> GSM152865 1 0.0324 0.8915 0.992 0.000 0.000 0.004 0.004
#> GSM152866 1 0.3196 0.8693 0.804 0.000 0.192 0.000 0.004
#> GSM152867 1 0.0324 0.8915 0.992 0.000 0.000 0.004 0.004
#> GSM152868 1 0.0324 0.8915 0.992 0.000 0.000 0.004 0.004
#> GSM152869 1 0.0324 0.8915 0.992 0.000 0.000 0.004 0.004
#> GSM152870 1 0.3314 0.8587 0.852 0.000 0.108 0.020 0.020
#> GSM152871 1 0.3314 0.8587 0.852 0.000 0.108 0.020 0.020
#> GSM152872 1 0.3314 0.8587 0.852 0.000 0.108 0.020 0.020
#> GSM152873 1 0.2629 0.8812 0.860 0.000 0.136 0.000 0.004
#> GSM152874 1 0.2629 0.8812 0.860 0.000 0.136 0.000 0.004
#> GSM152875 1 0.2629 0.8812 0.860 0.000 0.136 0.000 0.004
#> GSM152876 1 0.2583 0.8816 0.864 0.000 0.132 0.000 0.004
#> GSM152877 1 0.2629 0.8812 0.860 0.000 0.136 0.000 0.004
#> GSM152878 1 0.2629 0.8812 0.860 0.000 0.136 0.000 0.004
#> GSM152879 1 0.2583 0.8816 0.864 0.000 0.132 0.000 0.004
#> GSM152880 1 0.2583 0.8816 0.864 0.000 0.132 0.000 0.004
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.1826 0.7591 0.000 0.924 0.020 0.052 0.000 0.004
#> GSM152805 5 0.0405 0.7831 0.000 0.004 0.000 0.000 0.988 0.008
#> GSM152806 5 0.0000 0.7865 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152807 2 0.2706 0.7795 0.000 0.832 0.000 0.160 0.000 0.008
#> GSM152808 5 0.0000 0.7865 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152809 2 0.2706 0.7795 0.000 0.832 0.000 0.160 0.000 0.008
#> GSM152810 6 0.5051 0.5105 0.000 0.000 0.048 0.024 0.324 0.604
#> GSM152811 5 0.2736 0.7116 0.000 0.000 0.076 0.020 0.876 0.028
#> GSM152812 2 0.2706 0.7795 0.000 0.832 0.000 0.160 0.000 0.008
#> GSM152813 2 0.0909 0.7362 0.000 0.968 0.020 0.012 0.000 0.000
#> GSM152814 2 0.0806 0.7333 0.000 0.972 0.020 0.008 0.000 0.000
#> GSM152815 2 0.2706 0.7795 0.000 0.832 0.000 0.160 0.000 0.008
#> GSM152816 3 0.5537 0.7612 0.000 0.432 0.468 0.000 0.084 0.016
#> GSM152817 5 0.0000 0.7865 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152818 5 0.0000 0.7865 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152819 2 0.4024 0.5227 0.000 0.784 0.080 0.000 0.116 0.020
#> GSM152820 2 0.4687 0.1352 0.000 0.704 0.216 0.004 0.056 0.020
#> GSM152821 2 0.1080 0.7579 0.000 0.960 0.004 0.032 0.000 0.004
#> GSM153115 4 0.1075 0.8867 0.000 0.048 0.000 0.952 0.000 0.000
#> GSM153116 5 0.2146 0.7300 0.000 0.060 0.024 0.000 0.908 0.008
#> GSM153117 5 0.5782 0.0718 0.000 0.380 0.140 0.000 0.472 0.008
#> GSM153118 2 0.0748 0.7296 0.000 0.976 0.016 0.004 0.000 0.004
#> GSM153119 6 0.4379 0.4653 0.000 0.000 0.028 0.000 0.396 0.576
#> GSM153120 6 0.4238 0.1943 0.000 0.016 0.000 0.444 0.000 0.540
#> GSM153121 3 0.5270 0.8886 0.000 0.284 0.612 0.000 0.084 0.020
#> GSM153122 6 0.4518 0.6660 0.000 0.000 0.080 0.004 0.220 0.696
#> GSM153123 2 0.4124 -0.1940 0.000 0.644 0.332 0.000 0.000 0.024
#> GSM153124 4 0.1075 0.8867 0.000 0.048 0.000 0.952 0.000 0.000
#> GSM153125 4 0.1075 0.8867 0.000 0.048 0.000 0.952 0.000 0.000
#> GSM153126 3 0.4887 0.9005 0.000 0.300 0.612 0.000 0.088 0.000
#> GSM153127 2 0.2706 0.7795 0.000 0.832 0.000 0.160 0.000 0.008
#> GSM153128 6 0.4940 0.7108 0.000 0.060 0.096 0.020 0.076 0.748
#> GSM153129 3 0.4024 0.8478 0.000 0.400 0.592 0.000 0.004 0.004
#> GSM153130 3 0.4971 0.8974 0.000 0.300 0.604 0.000 0.096 0.000
#> GSM153131 3 0.5002 0.8987 0.000 0.332 0.588 0.000 0.076 0.004
#> GSM153132 3 0.5434 0.8041 0.000 0.416 0.496 0.000 0.068 0.020
#> GSM153133 2 0.2147 0.6500 0.000 0.896 0.084 0.000 0.000 0.020
#> GSM153134 3 0.3881 0.8459 0.000 0.396 0.600 0.000 0.000 0.004
#> GSM153135 2 0.2805 0.7783 0.000 0.828 0.000 0.160 0.000 0.012
#> GSM153136 4 0.1075 0.8867 0.000 0.048 0.000 0.952 0.000 0.000
#> GSM153137 2 0.4596 0.6304 0.000 0.692 0.000 0.188 0.000 0.120
#> GSM153138 2 0.5347 0.3942 0.000 0.560 0.000 0.136 0.000 0.304
#> GSM153139 3 0.4918 0.9020 0.000 0.308 0.604 0.000 0.088 0.000
#> GSM153140 2 0.2502 0.7689 0.000 0.884 0.020 0.084 0.000 0.012
#> GSM153141 2 0.3315 0.7670 0.000 0.804 0.000 0.156 0.000 0.040
#> GSM153142 5 0.0405 0.7828 0.000 0.000 0.008 0.000 0.988 0.004
#> GSM153143 2 0.2778 0.7747 0.000 0.824 0.000 0.168 0.000 0.008
#> GSM153144 2 0.3789 -0.4628 0.000 0.584 0.416 0.000 0.000 0.000
#> GSM153145 5 0.0000 0.7865 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153146 2 0.0951 0.7507 0.000 0.968 0.004 0.020 0.000 0.008
#> GSM153147 3 0.3945 0.8571 0.000 0.380 0.612 0.000 0.008 0.000
#> GSM153148 2 0.2706 0.7795 0.000 0.832 0.000 0.160 0.000 0.008
#> GSM153149 2 0.0909 0.7217 0.000 0.968 0.020 0.000 0.000 0.012
#> GSM153150 4 0.3101 0.6179 0.000 0.000 0.000 0.756 0.000 0.244
#> GSM153151 6 0.4777 0.6564 0.000 0.120 0.124 0.024 0.004 0.728
#> GSM153152 3 0.3966 0.7730 0.000 0.444 0.552 0.000 0.000 0.004
#> GSM153153 2 0.0837 0.7262 0.000 0.972 0.020 0.004 0.000 0.004
#> GSM153154 3 0.5126 0.9000 0.000 0.312 0.596 0.000 0.084 0.008
#> GSM153155 2 0.2306 0.7733 0.000 0.888 0.016 0.092 0.000 0.004
#> GSM153156 3 0.5378 0.8862 0.000 0.292 0.600 0.000 0.084 0.024
#> GSM153157 5 0.3374 0.6765 0.000 0.016 0.132 0.004 0.824 0.024
#> GSM153158 5 0.5981 -0.0121 0.000 0.256 0.232 0.000 0.504 0.008
#> GSM153159 5 0.0935 0.7745 0.000 0.000 0.032 0.000 0.964 0.004
#> GSM153160 3 0.4913 0.8983 0.000 0.296 0.612 0.000 0.092 0.000
#> GSM153161 2 0.3736 0.7411 0.000 0.776 0.000 0.156 0.000 0.068
#> GSM153162 3 0.4493 0.8890 0.000 0.344 0.612 0.000 0.044 0.000
#> GSM153163 3 0.4918 0.9020 0.000 0.308 0.604 0.000 0.088 0.000
#> GSM153164 5 0.5912 0.0377 0.000 0.404 0.132 0.000 0.448 0.016
#> GSM153165 3 0.4918 0.9020 0.000 0.308 0.604 0.000 0.088 0.000
#> GSM153166 2 0.3161 0.3334 0.000 0.776 0.216 0.000 0.000 0.008
#> GSM153167 3 0.4089 0.7413 0.000 0.468 0.524 0.000 0.000 0.008
#> GSM153168 5 0.0000 0.7865 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153169 3 0.5105 0.8972 0.000 0.300 0.600 0.000 0.096 0.004
#> GSM153170 3 0.4795 0.9004 0.000 0.324 0.604 0.000 0.072 0.000
#> GSM153171 4 0.0993 0.8826 0.000 0.024 0.000 0.964 0.000 0.012
#> GSM153172 2 0.0777 0.7257 0.000 0.972 0.024 0.004 0.000 0.000
#> GSM153173 3 0.4918 0.9020 0.000 0.308 0.604 0.000 0.088 0.000
#> GSM153174 3 0.3727 0.8473 0.000 0.388 0.612 0.000 0.000 0.000
#> GSM153175 4 0.1341 0.8761 0.000 0.028 0.024 0.948 0.000 0.000
#> GSM153176 4 0.2451 0.7786 0.000 0.056 0.060 0.884 0.000 0.000
#> GSM153177 2 0.2312 0.5865 0.000 0.876 0.112 0.000 0.000 0.012
#> GSM152931 4 0.1075 0.8867 0.000 0.048 0.000 0.952 0.000 0.000
#> GSM152932 2 0.1483 0.7172 0.000 0.944 0.036 0.008 0.000 0.012
#> GSM152933 2 0.0935 0.7074 0.000 0.964 0.032 0.000 0.000 0.004
#> GSM152934 6 0.3670 0.5787 0.000 0.012 0.000 0.284 0.000 0.704
#> GSM152935 6 0.4980 0.6890 0.000 0.080 0.040 0.008 0.152 0.720
#> GSM152936 4 0.1713 0.8671 0.000 0.028 0.000 0.928 0.000 0.044
#> GSM152937 6 0.4696 0.7111 0.000 0.040 0.116 0.020 0.064 0.760
#> GSM152938 6 0.4546 0.6200 0.000 0.064 0.204 0.004 0.012 0.716
#> GSM152939 4 0.3500 0.6617 0.000 0.028 0.204 0.768 0.000 0.000
#> GSM152940 4 0.3351 0.5384 0.000 0.000 0.000 0.712 0.000 0.288
#> GSM152941 4 0.6399 0.3097 0.100 0.000 0.180 0.568 0.000 0.152
#> GSM152942 3 0.5262 0.8866 0.000 0.292 0.612 0.028 0.068 0.000
#> GSM152943 6 0.3992 0.6644 0.000 0.072 0.000 0.180 0.000 0.748
#> GSM152944 3 0.4918 0.9020 0.000 0.308 0.604 0.000 0.088 0.000
#> GSM152945 6 0.3773 0.6954 0.000 0.012 0.008 0.028 0.164 0.788
#> GSM152946 2 0.3628 0.7618 0.000 0.784 0.004 0.168 0.000 0.044
#> GSM152947 4 0.3607 0.4103 0.000 0.000 0.000 0.652 0.000 0.348
#> GSM152948 2 0.2706 0.7795 0.000 0.832 0.000 0.160 0.000 0.008
#> GSM152949 3 0.4580 0.8940 0.000 0.336 0.612 0.000 0.052 0.000
#> GSM152950 3 0.4953 0.8132 0.000 0.420 0.528 0.000 0.036 0.016
#> GSM152951 2 0.2706 0.7795 0.000 0.832 0.000 0.160 0.000 0.008
#> GSM152952 2 0.3681 0.7431 0.000 0.780 0.000 0.156 0.000 0.064
#> GSM152953 2 0.3588 0.7555 0.000 0.788 0.000 0.152 0.000 0.060
#> GSM152954 4 0.0777 0.8834 0.000 0.024 0.000 0.972 0.000 0.004
#> GSM152955 6 0.5396 0.4206 0.000 0.004 0.008 0.076 0.404 0.508
#> GSM152956 2 0.2805 0.7783 0.000 0.828 0.000 0.160 0.000 0.012
#> GSM152957 4 0.0935 0.8855 0.000 0.032 0.000 0.964 0.000 0.004
#> GSM152958 4 0.1007 0.8868 0.000 0.044 0.000 0.956 0.000 0.000
#> GSM152959 4 0.0692 0.8818 0.000 0.020 0.000 0.976 0.000 0.004
#> GSM152960 4 0.2190 0.8396 0.000 0.040 0.000 0.900 0.000 0.060
#> GSM152961 4 0.0858 0.8850 0.000 0.028 0.000 0.968 0.000 0.004
#> GSM152962 6 0.4602 0.6476 0.000 0.084 0.164 0.008 0.012 0.732
#> GSM152963 2 0.3645 0.7475 0.000 0.784 0.000 0.152 0.000 0.064
#> GSM152964 6 0.3999 0.6698 0.000 0.000 0.024 0.020 0.212 0.744
#> GSM152965 2 0.4319 0.4135 0.000 0.620 0.000 0.032 0.000 0.348
#> GSM152966 4 0.1075 0.8867 0.000 0.048 0.000 0.952 0.000 0.000
#> GSM152967 2 0.1065 0.7470 0.000 0.964 0.008 0.020 0.000 0.008
#> GSM152968 3 0.4606 0.8932 0.000 0.344 0.604 0.000 0.052 0.000
#> GSM152969 4 0.1075 0.8867 0.000 0.048 0.000 0.952 0.000 0.000
#> GSM152970 4 0.1265 0.8598 0.000 0.008 0.000 0.948 0.000 0.044
#> GSM152971 4 0.1075 0.8867 0.000 0.048 0.000 0.952 0.000 0.000
#> GSM152972 4 0.1075 0.8867 0.000 0.048 0.000 0.952 0.000 0.000
#> GSM152973 3 0.5373 0.6729 0.000 0.216 0.588 0.196 0.000 0.000
#> GSM152974 2 0.0806 0.7296 0.000 0.972 0.020 0.000 0.000 0.008
#> GSM152975 4 0.5088 0.0838 0.000 0.412 0.004 0.516 0.000 0.068
#> GSM152976 4 0.1010 0.8861 0.000 0.036 0.000 0.960 0.000 0.004
#> GSM152977 4 0.1434 0.8723 0.000 0.028 0.012 0.948 0.000 0.012
#> GSM152978 4 0.0777 0.8834 0.000 0.024 0.000 0.972 0.000 0.004
#> GSM152979 3 0.4902 0.9007 0.000 0.304 0.608 0.000 0.088 0.000
#> GSM152980 4 0.4729 -0.0854 0.000 0.464 0.016 0.500 0.000 0.020
#> GSM152981 5 0.0458 0.7815 0.000 0.000 0.016 0.000 0.984 0.000
#> GSM152982 4 0.1461 0.8827 0.000 0.044 0.016 0.940 0.000 0.000
#> GSM152983 4 0.1075 0.8867 0.000 0.048 0.000 0.952 0.000 0.000
#> GSM152984 3 0.4702 0.8548 0.000 0.332 0.612 0.052 0.004 0.000
#> GSM152985 4 0.0964 0.8740 0.000 0.016 0.012 0.968 0.000 0.004
#> GSM152986 4 0.1075 0.8867 0.000 0.048 0.000 0.952 0.000 0.000
#> GSM152987 6 0.3935 0.5914 0.012 0.000 0.152 0.060 0.000 0.776
#> GSM152988 3 0.5903 0.2780 0.000 0.204 0.400 0.396 0.000 0.000
#> GSM152989 4 0.0692 0.8818 0.000 0.020 0.000 0.976 0.000 0.004
#> GSM152990 3 0.4874 0.9023 0.000 0.308 0.608 0.000 0.084 0.000
#> GSM152991 2 0.6521 0.2870 0.000 0.572 0.120 0.004 0.144 0.160
#> GSM187524 1 0.6259 0.6737 0.488 0.000 0.284 0.024 0.000 0.204
#> GSM187525 1 0.6239 0.6775 0.492 0.000 0.284 0.024 0.000 0.200
#> GSM187526 1 0.6218 0.6817 0.496 0.000 0.284 0.024 0.000 0.196
#> GSM187527 1 0.0000 0.8396 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152856 1 0.0000 0.8396 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152857 1 0.0000 0.8396 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152858 1 0.4909 0.8059 0.664 0.000 0.236 0.012 0.000 0.088
#> GSM152859 1 0.6206 0.6699 0.480 0.000 0.304 0.020 0.000 0.196
#> GSM152860 1 0.4909 0.8059 0.664 0.000 0.236 0.012 0.000 0.088
#> GSM152861 1 0.3701 0.8471 0.804 0.000 0.112 0.012 0.000 0.072
#> GSM152862 1 0.4909 0.8059 0.664 0.000 0.236 0.012 0.000 0.088
#> GSM152863 1 0.3240 0.8506 0.840 0.000 0.092 0.012 0.000 0.056
#> GSM152864 1 0.3442 0.8500 0.824 0.000 0.104 0.012 0.000 0.060
#> GSM152865 1 0.3442 0.8500 0.824 0.000 0.104 0.012 0.000 0.060
#> GSM152866 1 0.1789 0.8202 0.924 0.000 0.032 0.000 0.000 0.044
#> GSM152867 1 0.3442 0.8500 0.824 0.000 0.104 0.012 0.000 0.060
#> GSM152868 1 0.3442 0.8500 0.824 0.000 0.104 0.012 0.000 0.060
#> GSM152869 1 0.3442 0.8500 0.824 0.000 0.104 0.012 0.000 0.060
#> GSM152870 1 0.4909 0.8059 0.664 0.000 0.236 0.012 0.000 0.088
#> GSM152871 1 0.4909 0.8059 0.664 0.000 0.236 0.012 0.000 0.088
#> GSM152872 1 0.4909 0.8059 0.664 0.000 0.236 0.012 0.000 0.088
#> GSM152873 1 0.0508 0.8375 0.984 0.000 0.004 0.000 0.000 0.012
#> GSM152874 1 0.0508 0.8375 0.984 0.000 0.004 0.000 0.000 0.012
#> GSM152875 1 0.0508 0.8375 0.984 0.000 0.004 0.000 0.000 0.012
#> GSM152876 1 0.0000 0.8396 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152877 1 0.0508 0.8375 0.984 0.000 0.004 0.000 0.000 0.012
#> GSM152878 1 0.0405 0.8381 0.988 0.000 0.004 0.000 0.000 0.008
#> GSM152879 1 0.0000 0.8396 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.8396 1.000 0.000 0.000 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> CV:kmeans 169 1.38e-28 2
#> CV:kmeans 164 1.93e-27 3
#> CV:kmeans 127 4.52e-26 4
#> CV:kmeans 88 7.16e-23 5
#> CV:kmeans 153 1.23e-30 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "skmeans"]
# you can also extract it by
# res = res_list["CV:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.964 0.985 0.4832 0.518 0.518
#> 3 3 0.664 0.787 0.901 0.3806 0.720 0.504
#> 4 4 0.604 0.695 0.807 0.1143 0.885 0.672
#> 5 5 0.684 0.700 0.826 0.0718 0.877 0.576
#> 6 6 0.683 0.606 0.774 0.0376 0.973 0.867
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.985 0.000 1.000
#> GSM152805 2 0.0000 0.985 0.000 1.000
#> GSM152806 2 0.0000 0.985 0.000 1.000
#> GSM152807 2 0.0000 0.985 0.000 1.000
#> GSM152808 2 0.0000 0.985 0.000 1.000
#> GSM152809 2 0.0000 0.985 0.000 1.000
#> GSM152810 1 0.0000 0.983 1.000 0.000
#> GSM152811 2 0.0000 0.985 0.000 1.000
#> GSM152812 2 0.0000 0.985 0.000 1.000
#> GSM152813 2 0.0000 0.985 0.000 1.000
#> GSM152814 2 0.0000 0.985 0.000 1.000
#> GSM152815 2 0.0000 0.985 0.000 1.000
#> GSM152816 2 0.0000 0.985 0.000 1.000
#> GSM152817 2 0.0000 0.985 0.000 1.000
#> GSM152818 2 0.0000 0.985 0.000 1.000
#> GSM152819 2 0.0000 0.985 0.000 1.000
#> GSM152820 2 0.0000 0.985 0.000 1.000
#> GSM152821 2 0.0000 0.985 0.000 1.000
#> GSM153115 1 0.0000 0.983 1.000 0.000
#> GSM153116 2 0.0000 0.985 0.000 1.000
#> GSM153117 2 0.0000 0.985 0.000 1.000
#> GSM153118 2 0.0000 0.985 0.000 1.000
#> GSM153119 2 0.0000 0.985 0.000 1.000
#> GSM153120 1 0.0000 0.983 1.000 0.000
#> GSM153121 2 0.0000 0.985 0.000 1.000
#> GSM153122 2 0.0000 0.985 0.000 1.000
#> GSM153123 2 0.0000 0.985 0.000 1.000
#> GSM153124 2 0.8499 0.623 0.276 0.724
#> GSM153125 1 0.0376 0.980 0.996 0.004
#> GSM153126 2 0.0000 0.985 0.000 1.000
#> GSM153127 2 0.0000 0.985 0.000 1.000
#> GSM153128 2 0.0000 0.985 0.000 1.000
#> GSM153129 2 0.0000 0.985 0.000 1.000
#> GSM153130 2 0.0000 0.985 0.000 1.000
#> GSM153131 2 0.0000 0.985 0.000 1.000
#> GSM153132 2 0.0000 0.985 0.000 1.000
#> GSM153133 2 0.0000 0.985 0.000 1.000
#> GSM153134 2 0.0000 0.985 0.000 1.000
#> GSM153135 2 0.0000 0.985 0.000 1.000
#> GSM153136 1 0.0000 0.983 1.000 0.000
#> GSM153137 1 0.7815 0.699 0.768 0.232
#> GSM153138 2 0.0000 0.985 0.000 1.000
#> GSM153139 2 0.0000 0.985 0.000 1.000
#> GSM153140 2 0.0000 0.985 0.000 1.000
#> GSM153141 2 0.0000 0.985 0.000 1.000
#> GSM153142 2 0.0000 0.985 0.000 1.000
#> GSM153143 2 0.0000 0.985 0.000 1.000
#> GSM153144 2 0.0000 0.985 0.000 1.000
#> GSM153145 2 0.0000 0.985 0.000 1.000
#> GSM153146 2 0.0000 0.985 0.000 1.000
#> GSM153147 2 0.0000 0.985 0.000 1.000
#> GSM153148 2 0.0000 0.985 0.000 1.000
#> GSM153149 2 0.0000 0.985 0.000 1.000
#> GSM153150 1 0.0000 0.983 1.000 0.000
#> GSM153151 2 0.0000 0.985 0.000 1.000
#> GSM153152 2 0.0000 0.985 0.000 1.000
#> GSM153153 2 0.0000 0.985 0.000 1.000
#> GSM153154 2 0.0000 0.985 0.000 1.000
#> GSM153155 2 0.0000 0.985 0.000 1.000
#> GSM153156 2 0.0000 0.985 0.000 1.000
#> GSM153157 2 0.0000 0.985 0.000 1.000
#> GSM153158 2 0.0000 0.985 0.000 1.000
#> GSM153159 2 0.0000 0.985 0.000 1.000
#> GSM153160 2 0.0000 0.985 0.000 1.000
#> GSM153161 2 0.0000 0.985 0.000 1.000
#> GSM153162 2 0.0000 0.985 0.000 1.000
#> GSM153163 2 0.0000 0.985 0.000 1.000
#> GSM153164 2 0.0000 0.985 0.000 1.000
#> GSM153165 2 0.0000 0.985 0.000 1.000
#> GSM153166 2 0.0000 0.985 0.000 1.000
#> GSM153167 2 0.0000 0.985 0.000 1.000
#> GSM153168 2 0.0000 0.985 0.000 1.000
#> GSM153169 2 0.0000 0.985 0.000 1.000
#> GSM153170 2 0.0000 0.985 0.000 1.000
#> GSM153171 1 0.0000 0.983 1.000 0.000
#> GSM153172 2 0.0000 0.985 0.000 1.000
#> GSM153173 2 0.0000 0.985 0.000 1.000
#> GSM153174 2 0.0000 0.985 0.000 1.000
#> GSM153175 1 0.0000 0.983 1.000 0.000
#> GSM153176 1 0.0000 0.983 1.000 0.000
#> GSM153177 2 0.0000 0.985 0.000 1.000
#> GSM152931 1 0.0000 0.983 1.000 0.000
#> GSM152932 2 0.0000 0.985 0.000 1.000
#> GSM152933 2 0.0000 0.985 0.000 1.000
#> GSM152934 1 0.3584 0.918 0.932 0.068
#> GSM152935 2 0.0000 0.985 0.000 1.000
#> GSM152936 1 0.0000 0.983 1.000 0.000
#> GSM152937 2 0.8443 0.622 0.272 0.728
#> GSM152938 2 0.0000 0.985 0.000 1.000
#> GSM152939 1 0.9954 0.133 0.540 0.460
#> GSM152940 1 0.0000 0.983 1.000 0.000
#> GSM152941 1 0.0000 0.983 1.000 0.000
#> GSM152942 2 0.0000 0.985 0.000 1.000
#> GSM152943 1 0.3879 0.909 0.924 0.076
#> GSM152944 2 0.0000 0.985 0.000 1.000
#> GSM152945 2 0.8661 0.592 0.288 0.712
#> GSM152946 2 0.0376 0.982 0.004 0.996
#> GSM152947 1 0.0000 0.983 1.000 0.000
#> GSM152948 2 0.0000 0.985 0.000 1.000
#> GSM152949 2 0.0000 0.985 0.000 1.000
#> GSM152950 2 0.0000 0.985 0.000 1.000
#> GSM152951 2 0.0000 0.985 0.000 1.000
#> GSM152952 2 0.0000 0.985 0.000 1.000
#> GSM152953 2 0.0000 0.985 0.000 1.000
#> GSM152954 1 0.0000 0.983 1.000 0.000
#> GSM152955 2 0.0376 0.982 0.004 0.996
#> GSM152956 2 0.0000 0.985 0.000 1.000
#> GSM152957 1 0.0000 0.983 1.000 0.000
#> GSM152958 1 0.0000 0.983 1.000 0.000
#> GSM152959 1 0.0000 0.983 1.000 0.000
#> GSM152960 1 0.0000 0.983 1.000 0.000
#> GSM152961 1 0.0000 0.983 1.000 0.000
#> GSM152962 2 0.0000 0.985 0.000 1.000
#> GSM152963 2 0.0000 0.985 0.000 1.000
#> GSM152964 1 0.7883 0.692 0.764 0.236
#> GSM152965 2 0.0000 0.985 0.000 1.000
#> GSM152966 1 0.0000 0.983 1.000 0.000
#> GSM152967 2 0.0000 0.985 0.000 1.000
#> GSM152968 2 0.0000 0.985 0.000 1.000
#> GSM152969 1 0.0000 0.983 1.000 0.000
#> GSM152970 1 0.0000 0.983 1.000 0.000
#> GSM152971 1 0.0000 0.983 1.000 0.000
#> GSM152972 1 0.0000 0.983 1.000 0.000
#> GSM152973 2 0.8763 0.584 0.296 0.704
#> GSM152974 2 0.0000 0.985 0.000 1.000
#> GSM152975 2 0.0376 0.982 0.004 0.996
#> GSM152976 1 0.0000 0.983 1.000 0.000
#> GSM152977 1 0.0000 0.983 1.000 0.000
#> GSM152978 1 0.0000 0.983 1.000 0.000
#> GSM152979 2 0.0000 0.985 0.000 1.000
#> GSM152980 2 0.0000 0.985 0.000 1.000
#> GSM152981 2 0.0000 0.985 0.000 1.000
#> GSM152982 1 0.0672 0.976 0.992 0.008
#> GSM152983 1 0.0000 0.983 1.000 0.000
#> GSM152984 2 0.0000 0.985 0.000 1.000
#> GSM152985 1 0.0000 0.983 1.000 0.000
#> GSM152986 1 0.0000 0.983 1.000 0.000
#> GSM152987 1 0.0000 0.983 1.000 0.000
#> GSM152988 2 0.9087 0.526 0.324 0.676
#> GSM152989 1 0.0000 0.983 1.000 0.000
#> GSM152990 2 0.0000 0.985 0.000 1.000
#> GSM152991 2 0.0000 0.985 0.000 1.000
#> GSM187524 1 0.0000 0.983 1.000 0.000
#> GSM187525 1 0.0000 0.983 1.000 0.000
#> GSM187526 1 0.0000 0.983 1.000 0.000
#> GSM187527 1 0.0000 0.983 1.000 0.000
#> GSM152856 1 0.0000 0.983 1.000 0.000
#> GSM152857 1 0.0000 0.983 1.000 0.000
#> GSM152858 1 0.0000 0.983 1.000 0.000
#> GSM152859 1 0.0000 0.983 1.000 0.000
#> GSM152860 1 0.0000 0.983 1.000 0.000
#> GSM152861 1 0.0000 0.983 1.000 0.000
#> GSM152862 1 0.0000 0.983 1.000 0.000
#> GSM152863 1 0.0000 0.983 1.000 0.000
#> GSM152864 1 0.0000 0.983 1.000 0.000
#> GSM152865 1 0.0000 0.983 1.000 0.000
#> GSM152866 1 0.0000 0.983 1.000 0.000
#> GSM152867 1 0.0000 0.983 1.000 0.000
#> GSM152868 1 0.0000 0.983 1.000 0.000
#> GSM152869 1 0.0000 0.983 1.000 0.000
#> GSM152870 1 0.0000 0.983 1.000 0.000
#> GSM152871 1 0.0000 0.983 1.000 0.000
#> GSM152872 1 0.0000 0.983 1.000 0.000
#> GSM152873 1 0.0000 0.983 1.000 0.000
#> GSM152874 1 0.0000 0.983 1.000 0.000
#> GSM152875 1 0.0000 0.983 1.000 0.000
#> GSM152876 1 0.0000 0.983 1.000 0.000
#> GSM152877 1 0.0000 0.983 1.000 0.000
#> GSM152878 1 0.0000 0.983 1.000 0.000
#> GSM152879 1 0.0000 0.983 1.000 0.000
#> GSM152880 1 0.0000 0.983 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.0237 0.83974 0.000 0.996 0.004
#> GSM152805 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM152806 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM152807 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM152808 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM152809 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM152810 1 0.5363 0.61681 0.724 0.000 0.276
#> GSM152811 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM152812 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM152813 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM152814 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM152815 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM152816 3 0.3752 0.84373 0.000 0.144 0.856
#> GSM152817 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM152818 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM152819 3 0.3941 0.80988 0.000 0.156 0.844
#> GSM152820 3 0.3941 0.82291 0.000 0.156 0.844
#> GSM152821 2 0.1031 0.83409 0.000 0.976 0.024
#> GSM153115 2 0.4796 0.66562 0.220 0.780 0.000
#> GSM153116 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM153117 3 0.2066 0.89033 0.000 0.060 0.940
#> GSM153118 2 0.4750 0.69540 0.000 0.784 0.216
#> GSM153119 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM153120 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM153121 3 0.1753 0.90548 0.000 0.048 0.952
#> GSM153122 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM153123 2 0.6225 0.25257 0.000 0.568 0.432
#> GSM153124 2 0.3532 0.78403 0.108 0.884 0.008
#> GSM153125 2 0.2537 0.80389 0.080 0.920 0.000
#> GSM153126 3 0.1753 0.90548 0.000 0.048 0.952
#> GSM153127 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM153128 3 0.0983 0.90833 0.004 0.016 0.980
#> GSM153129 3 0.6045 0.43436 0.000 0.380 0.620
#> GSM153130 3 0.1529 0.90783 0.000 0.040 0.960
#> GSM153131 3 0.1031 0.91115 0.000 0.024 0.976
#> GSM153132 3 0.2625 0.88868 0.000 0.084 0.916
#> GSM153133 2 0.3686 0.77018 0.000 0.860 0.140
#> GSM153134 2 0.6309 0.00666 0.000 0.504 0.496
#> GSM153135 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM153136 2 0.6192 0.26793 0.420 0.580 0.000
#> GSM153137 2 0.1315 0.83339 0.020 0.972 0.008
#> GSM153138 2 0.4047 0.77611 0.004 0.848 0.148
#> GSM153139 3 0.1529 0.90783 0.000 0.040 0.960
#> GSM153140 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM153141 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM153142 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM153143 2 0.0237 0.83951 0.000 0.996 0.004
#> GSM153144 2 0.0237 0.83963 0.000 0.996 0.004
#> GSM153145 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM153146 2 0.2066 0.81918 0.000 0.940 0.060
#> GSM153147 3 0.5785 0.53809 0.000 0.332 0.668
#> GSM153148 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM153149 2 0.4842 0.66679 0.000 0.776 0.224
#> GSM153150 1 0.0892 0.90970 0.980 0.020 0.000
#> GSM153151 3 0.4346 0.79889 0.000 0.184 0.816
#> GSM153152 2 0.6274 0.15158 0.000 0.544 0.456
#> GSM153153 2 0.3116 0.78848 0.000 0.892 0.108
#> GSM153154 3 0.1289 0.90942 0.000 0.032 0.968
#> GSM153155 2 0.2878 0.80177 0.000 0.904 0.096
#> GSM153156 3 0.1860 0.90401 0.000 0.052 0.948
#> GSM153157 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM153158 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM153159 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM153160 3 0.1163 0.91015 0.000 0.028 0.972
#> GSM153161 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM153162 3 0.5882 0.49841 0.000 0.348 0.652
#> GSM153163 3 0.1529 0.90783 0.000 0.040 0.960
#> GSM153164 3 0.2711 0.87076 0.000 0.088 0.912
#> GSM153165 3 0.1860 0.90401 0.000 0.052 0.948
#> GSM153166 2 0.5291 0.59837 0.000 0.732 0.268
#> GSM153167 2 0.5948 0.42276 0.000 0.640 0.360
#> GSM153168 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM153169 3 0.0892 0.91085 0.000 0.020 0.980
#> GSM153170 3 0.2356 0.89555 0.000 0.072 0.928
#> GSM153171 1 0.4504 0.73429 0.804 0.196 0.000
#> GSM153172 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM153173 3 0.1860 0.90401 0.000 0.052 0.948
#> GSM153174 2 0.4842 0.68295 0.000 0.776 0.224
#> GSM153175 2 0.5896 0.56328 0.292 0.700 0.008
#> GSM153176 1 0.6079 0.35405 0.612 0.000 0.388
#> GSM153177 2 0.6126 0.32264 0.000 0.600 0.400
#> GSM152931 2 0.4346 0.70977 0.184 0.816 0.000
#> GSM152932 2 0.2537 0.80859 0.000 0.920 0.080
#> GSM152933 2 0.6302 0.03279 0.000 0.520 0.480
#> GSM152934 1 0.7750 0.59802 0.676 0.140 0.184
#> GSM152935 3 0.0237 0.90969 0.000 0.004 0.996
#> GSM152936 1 0.6286 0.12182 0.536 0.464 0.000
#> GSM152937 3 0.2356 0.86031 0.072 0.000 0.928
#> GSM152938 3 0.0592 0.91053 0.000 0.012 0.988
#> GSM152939 2 0.3993 0.80606 0.052 0.884 0.064
#> GSM152940 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152941 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152942 3 0.2165 0.89849 0.000 0.064 0.936
#> GSM152943 1 0.6723 0.60855 0.704 0.248 0.048
#> GSM152944 3 0.1643 0.90691 0.000 0.044 0.956
#> GSM152945 3 0.4634 0.75719 0.164 0.012 0.824
#> GSM152946 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM152947 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152948 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM152949 3 0.3941 0.81989 0.000 0.156 0.844
#> GSM152950 3 0.4291 0.80209 0.000 0.180 0.820
#> GSM152951 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM152952 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM152953 2 0.0424 0.83833 0.000 0.992 0.008
#> GSM152954 1 0.4178 0.76684 0.828 0.172 0.000
#> GSM152955 3 0.0237 0.90969 0.000 0.004 0.996
#> GSM152956 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM152957 1 0.0747 0.91250 0.984 0.016 0.000
#> GSM152958 1 0.4654 0.71838 0.792 0.208 0.000
#> GSM152959 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152960 1 0.6062 0.38472 0.616 0.384 0.000
#> GSM152961 1 0.1860 0.88573 0.948 0.052 0.000
#> GSM152962 3 0.0237 0.91013 0.000 0.004 0.996
#> GSM152963 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM152964 3 0.4887 0.67544 0.228 0.000 0.772
#> GSM152965 2 0.4178 0.75390 0.000 0.828 0.172
#> GSM152966 2 0.3340 0.77420 0.120 0.880 0.000
#> GSM152967 2 0.0000 0.84026 0.000 1.000 0.000
#> GSM152968 3 0.3482 0.85294 0.000 0.128 0.872
#> GSM152969 2 0.5058 0.63158 0.244 0.756 0.000
#> GSM152970 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152971 2 0.6062 0.36562 0.384 0.616 0.000
#> GSM152972 2 0.5926 0.43158 0.356 0.644 0.000
#> GSM152973 3 0.7839 -0.00713 0.052 0.464 0.484
#> GSM152974 2 0.0892 0.83614 0.000 0.980 0.020
#> GSM152975 2 0.6075 0.58332 0.008 0.676 0.316
#> GSM152976 1 0.3112 0.84471 0.900 0.096 0.004
#> GSM152977 1 0.1129 0.90706 0.976 0.004 0.020
#> GSM152978 1 0.6008 0.43344 0.628 0.372 0.000
#> GSM152979 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM152980 2 0.4452 0.71846 0.000 0.808 0.192
#> GSM152981 3 0.0000 0.90989 0.000 0.000 1.000
#> GSM152982 2 0.9437 0.36180 0.300 0.492 0.208
#> GSM152983 2 0.6330 0.32987 0.396 0.600 0.004
#> GSM152984 3 0.5882 0.49113 0.000 0.348 0.652
#> GSM152985 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152986 1 0.6308 0.02477 0.508 0.492 0.000
#> GSM152987 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152988 2 0.4146 0.80148 0.044 0.876 0.080
#> GSM152989 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152990 3 0.1860 0.90401 0.000 0.052 0.948
#> GSM152991 3 0.2537 0.87382 0.000 0.080 0.920
#> GSM187524 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM187525 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM187526 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM187527 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152856 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152857 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152858 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152859 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152860 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152861 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152862 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152863 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152864 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152866 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152867 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152870 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152871 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152873 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152874 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152875 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152876 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152877 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152878 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152879 1 0.0000 0.92255 1.000 0.000 0.000
#> GSM152880 1 0.0000 0.92255 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.2714 0.8145 0.000 0.884 0.004 0.112
#> GSM152805 3 0.1109 0.7482 0.000 0.004 0.968 0.028
#> GSM152806 3 0.0000 0.7407 0.000 0.000 1.000 0.000
#> GSM152807 2 0.0592 0.8165 0.000 0.984 0.000 0.016
#> GSM152808 3 0.0000 0.7407 0.000 0.000 1.000 0.000
#> GSM152809 2 0.0707 0.8159 0.000 0.980 0.000 0.020
#> GSM152810 1 0.5292 0.2118 0.512 0.000 0.480 0.008
#> GSM152811 3 0.0000 0.7407 0.000 0.000 1.000 0.000
#> GSM152812 2 0.0592 0.8165 0.000 0.984 0.000 0.016
#> GSM152813 2 0.1716 0.8250 0.000 0.936 0.000 0.064
#> GSM152814 2 0.1940 0.8235 0.000 0.924 0.000 0.076
#> GSM152815 2 0.0469 0.8163 0.000 0.988 0.000 0.012
#> GSM152816 3 0.6808 0.6814 0.000 0.164 0.600 0.236
#> GSM152817 3 0.0000 0.7407 0.000 0.000 1.000 0.000
#> GSM152818 3 0.0000 0.7407 0.000 0.000 1.000 0.000
#> GSM152819 3 0.6014 0.3495 0.000 0.360 0.588 0.052
#> GSM152820 3 0.5941 0.5534 0.000 0.276 0.652 0.072
#> GSM152821 2 0.1975 0.8248 0.000 0.936 0.016 0.048
#> GSM153115 4 0.6058 0.7551 0.136 0.180 0.000 0.684
#> GSM153116 3 0.0000 0.7407 0.000 0.000 1.000 0.000
#> GSM153117 3 0.5753 0.5599 0.000 0.248 0.680 0.072
#> GSM153118 2 0.2892 0.8193 0.000 0.896 0.036 0.068
#> GSM153119 3 0.0469 0.7354 0.000 0.000 0.988 0.012
#> GSM153120 1 0.3587 0.7508 0.856 0.040 0.000 0.104
#> GSM153121 3 0.5331 0.7354 0.000 0.024 0.644 0.332
#> GSM153122 3 0.1302 0.7463 0.000 0.000 0.956 0.044
#> GSM153123 2 0.6522 0.5254 0.000 0.608 0.112 0.280
#> GSM153124 4 0.3925 0.6459 0.016 0.176 0.000 0.808
#> GSM153125 4 0.5573 0.6884 0.052 0.272 0.000 0.676
#> GSM153126 3 0.5386 0.7296 0.000 0.024 0.632 0.344
#> GSM153127 2 0.0469 0.8163 0.000 0.988 0.000 0.012
#> GSM153128 3 0.2773 0.7529 0.000 0.004 0.880 0.116
#> GSM153129 2 0.7924 -0.2503 0.000 0.340 0.328 0.332
#> GSM153130 3 0.5152 0.7417 0.000 0.020 0.664 0.316
#> GSM153131 3 0.5949 0.7395 0.000 0.068 0.644 0.288
#> GSM153132 3 0.6797 0.6845 0.000 0.160 0.600 0.240
#> GSM153133 2 0.4719 0.7541 0.000 0.772 0.048 0.180
#> GSM153134 2 0.7355 0.2889 0.000 0.488 0.172 0.340
#> GSM153135 2 0.0592 0.8165 0.000 0.984 0.000 0.016
#> GSM153136 4 0.6560 0.7352 0.212 0.128 0.008 0.652
#> GSM153137 2 0.1820 0.7901 0.020 0.944 0.000 0.036
#> GSM153138 2 0.4015 0.7384 0.000 0.832 0.116 0.052
#> GSM153139 3 0.5271 0.7397 0.000 0.024 0.656 0.320
#> GSM153140 2 0.2814 0.8056 0.000 0.868 0.000 0.132
#> GSM153141 2 0.0592 0.8165 0.000 0.984 0.000 0.016
#> GSM153142 3 0.0000 0.7407 0.000 0.000 1.000 0.000
#> GSM153143 2 0.1576 0.7994 0.000 0.948 0.004 0.048
#> GSM153144 2 0.4699 0.6483 0.000 0.676 0.004 0.320
#> GSM153145 3 0.0000 0.7407 0.000 0.000 1.000 0.000
#> GSM153146 2 0.1256 0.8244 0.000 0.964 0.008 0.028
#> GSM153147 3 0.7650 0.5163 0.000 0.212 0.424 0.364
#> GSM153148 2 0.0592 0.8165 0.000 0.984 0.000 0.016
#> GSM153149 2 0.3266 0.8104 0.000 0.868 0.024 0.108
#> GSM153150 1 0.5947 0.1435 0.584 0.024 0.012 0.380
#> GSM153151 3 0.7456 0.4203 0.000 0.308 0.492 0.200
#> GSM153152 2 0.7250 0.3302 0.000 0.504 0.160 0.336
#> GSM153153 2 0.2376 0.8214 0.000 0.916 0.016 0.068
#> GSM153154 3 0.5508 0.7541 0.000 0.056 0.692 0.252
#> GSM153155 2 0.2943 0.8194 0.000 0.892 0.032 0.076
#> GSM153156 3 0.5228 0.7446 0.000 0.024 0.664 0.312
#> GSM153157 3 0.0000 0.7407 0.000 0.000 1.000 0.000
#> GSM153158 3 0.2892 0.7562 0.000 0.036 0.896 0.068
#> GSM153159 3 0.0188 0.7420 0.000 0.000 0.996 0.004
#> GSM153160 3 0.5233 0.7353 0.000 0.020 0.648 0.332
#> GSM153161 2 0.0707 0.8126 0.000 0.980 0.000 0.020
#> GSM153162 3 0.7861 0.3799 0.000 0.272 0.368 0.360
#> GSM153163 3 0.5453 0.7387 0.000 0.032 0.648 0.320
#> GSM153164 3 0.5321 0.5926 0.000 0.228 0.716 0.056
#> GSM153165 3 0.5920 0.7226 0.000 0.052 0.612 0.336
#> GSM153166 2 0.4761 0.7461 0.000 0.768 0.048 0.184
#> GSM153167 2 0.7460 0.2495 0.000 0.468 0.184 0.348
#> GSM153168 3 0.0000 0.7407 0.000 0.000 1.000 0.000
#> GSM153169 3 0.4857 0.7508 0.000 0.016 0.700 0.284
#> GSM153170 3 0.6584 0.6923 0.000 0.096 0.568 0.336
#> GSM153171 4 0.6338 0.6331 0.316 0.084 0.000 0.600
#> GSM153172 2 0.2530 0.8153 0.000 0.888 0.000 0.112
#> GSM153173 3 0.5614 0.7298 0.000 0.036 0.628 0.336
#> GSM153174 2 0.6909 0.3987 0.000 0.520 0.116 0.364
#> GSM153175 4 0.2060 0.6430 0.016 0.052 0.000 0.932
#> GSM153176 4 0.6065 0.6022 0.176 0.000 0.140 0.684
#> GSM153177 2 0.5217 0.7260 0.000 0.756 0.108 0.136
#> GSM152931 4 0.6167 0.7458 0.116 0.220 0.000 0.664
#> GSM152932 2 0.3808 0.7820 0.000 0.812 0.012 0.176
#> GSM152933 2 0.4969 0.7278 0.000 0.772 0.140 0.088
#> GSM152934 1 0.9553 -0.1790 0.344 0.120 0.240 0.296
#> GSM152935 3 0.1488 0.7276 0.000 0.032 0.956 0.012
#> GSM152936 4 0.6393 0.7449 0.188 0.160 0.000 0.652
#> GSM152937 3 0.4412 0.7409 0.036 0.016 0.820 0.128
#> GSM152938 3 0.5038 0.7457 0.000 0.020 0.684 0.296
#> GSM152939 4 0.1792 0.6319 0.000 0.068 0.000 0.932
#> GSM152940 1 0.4804 0.5042 0.708 0.016 0.000 0.276
#> GSM152941 1 0.0188 0.8784 0.996 0.000 0.000 0.004
#> GSM152942 3 0.5506 0.6202 0.000 0.016 0.512 0.472
#> GSM152943 1 0.9175 -0.0632 0.392 0.336 0.112 0.160
#> GSM152944 3 0.5557 0.7426 0.000 0.040 0.652 0.308
#> GSM152945 3 0.5311 0.5865 0.100 0.072 0.788 0.040
#> GSM152946 2 0.3569 0.7407 0.000 0.804 0.000 0.196
#> GSM152947 1 0.4673 0.4718 0.700 0.008 0.000 0.292
#> GSM152948 2 0.0592 0.8165 0.000 0.984 0.000 0.016
#> GSM152949 3 0.7070 0.6432 0.000 0.136 0.516 0.348
#> GSM152950 3 0.7425 0.5892 0.000 0.212 0.508 0.280
#> GSM152951 2 0.0707 0.8147 0.000 0.980 0.000 0.020
#> GSM152952 2 0.0707 0.8137 0.000 0.980 0.000 0.020
#> GSM152953 2 0.0469 0.8163 0.000 0.988 0.000 0.012
#> GSM152954 4 0.6394 0.7115 0.244 0.120 0.000 0.636
#> GSM152955 3 0.1722 0.7150 0.000 0.008 0.944 0.048
#> GSM152956 2 0.0469 0.8163 0.000 0.988 0.000 0.012
#> GSM152957 4 0.5407 0.2658 0.484 0.012 0.000 0.504
#> GSM152958 4 0.6180 0.6591 0.296 0.080 0.000 0.624
#> GSM152959 1 0.4401 0.5200 0.724 0.004 0.000 0.272
#> GSM152960 4 0.7758 0.5041 0.292 0.272 0.000 0.436
#> GSM152961 4 0.6202 0.6399 0.312 0.076 0.000 0.612
#> GSM152962 3 0.4864 0.7552 0.000 0.060 0.768 0.172
#> GSM152963 2 0.0592 0.8155 0.000 0.984 0.000 0.016
#> GSM152964 3 0.3780 0.6004 0.148 0.004 0.832 0.016
#> GSM152965 2 0.3243 0.7934 0.000 0.876 0.088 0.036
#> GSM152966 4 0.5781 0.7143 0.072 0.252 0.000 0.676
#> GSM152967 2 0.2469 0.8221 0.000 0.892 0.000 0.108
#> GSM152968 3 0.7325 0.6063 0.000 0.168 0.492 0.340
#> GSM152969 4 0.6296 0.7345 0.112 0.244 0.000 0.644
#> GSM152970 1 0.3873 0.6110 0.772 0.000 0.000 0.228
#> GSM152971 4 0.6449 0.7389 0.204 0.152 0.000 0.644
#> GSM152972 4 0.6437 0.7463 0.168 0.184 0.000 0.648
#> GSM152973 4 0.2596 0.4702 0.000 0.024 0.068 0.908
#> GSM152974 2 0.3306 0.7919 0.000 0.840 0.004 0.156
#> GSM152975 3 0.7869 -0.0598 0.000 0.340 0.380 0.280
#> GSM152976 4 0.5954 0.6299 0.312 0.032 0.016 0.640
#> GSM152977 4 0.6725 0.6266 0.240 0.004 0.136 0.620
#> GSM152978 4 0.6808 0.7146 0.164 0.236 0.000 0.600
#> GSM152979 3 0.5085 0.7463 0.000 0.020 0.676 0.304
#> GSM152980 2 0.6797 0.2376 0.000 0.536 0.108 0.356
#> GSM152981 3 0.0188 0.7388 0.000 0.000 0.996 0.004
#> GSM152982 4 0.3146 0.6486 0.016 0.032 0.056 0.896
#> GSM152983 4 0.6556 0.7524 0.172 0.160 0.008 0.660
#> GSM152984 4 0.6466 -0.2794 0.000 0.104 0.288 0.608
#> GSM152985 1 0.4477 0.4342 0.688 0.000 0.000 0.312
#> GSM152986 4 0.6386 0.7338 0.212 0.140 0.000 0.648
#> GSM152987 1 0.0469 0.8728 0.988 0.000 0.000 0.012
#> GSM152988 4 0.1118 0.5902 0.000 0.036 0.000 0.964
#> GSM152989 1 0.3764 0.6304 0.784 0.000 0.000 0.216
#> GSM152990 3 0.5695 0.7289 0.000 0.040 0.624 0.336
#> GSM152991 3 0.2654 0.7174 0.000 0.108 0.888 0.004
#> GSM187524 1 0.0188 0.8784 0.996 0.000 0.000 0.004
#> GSM187525 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM187526 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM187527 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152856 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152857 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152858 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152859 1 0.0188 0.8784 0.996 0.000 0.000 0.004
#> GSM152860 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152861 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152862 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152863 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152864 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152866 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152867 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152868 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152870 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152871 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152872 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152873 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152875 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152876 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152877 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152878 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152879 1 0.0000 0.8811 1.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.8811 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.4153 0.7537 0.000 0.768 0.192 0.032 0.008
#> GSM152805 5 0.3861 0.6593 0.000 0.000 0.264 0.008 0.728
#> GSM152806 5 0.2690 0.7440 0.000 0.000 0.156 0.000 0.844
#> GSM152807 2 0.0693 0.8554 0.000 0.980 0.012 0.008 0.000
#> GSM152808 5 0.2773 0.7424 0.000 0.000 0.164 0.000 0.836
#> GSM152809 2 0.0693 0.8554 0.000 0.980 0.012 0.008 0.000
#> GSM152810 5 0.3734 0.6184 0.184 0.000 0.008 0.016 0.792
#> GSM152811 5 0.2806 0.7440 0.000 0.000 0.152 0.004 0.844
#> GSM152812 2 0.0566 0.8554 0.000 0.984 0.012 0.004 0.000
#> GSM152813 2 0.2233 0.8317 0.000 0.892 0.104 0.004 0.000
#> GSM152814 2 0.1768 0.8450 0.000 0.924 0.072 0.004 0.000
#> GSM152815 2 0.0451 0.8552 0.000 0.988 0.008 0.004 0.000
#> GSM152816 3 0.4581 0.6780 0.000 0.076 0.764 0.012 0.148
#> GSM152817 5 0.2813 0.7414 0.000 0.000 0.168 0.000 0.832
#> GSM152818 5 0.2852 0.7398 0.000 0.000 0.172 0.000 0.828
#> GSM152819 5 0.6879 0.3200 0.000 0.316 0.240 0.008 0.436
#> GSM152820 3 0.6917 -0.0176 0.000 0.152 0.452 0.028 0.368
#> GSM152821 2 0.0955 0.8535 0.000 0.968 0.028 0.000 0.004
#> GSM153115 4 0.2342 0.8185 0.024 0.040 0.020 0.916 0.000
#> GSM153116 5 0.3013 0.7440 0.000 0.008 0.160 0.000 0.832
#> GSM153117 5 0.6401 0.3282 0.000 0.184 0.336 0.000 0.480
#> GSM153118 2 0.3147 0.8203 0.000 0.856 0.112 0.008 0.024
#> GSM153119 5 0.2408 0.7337 0.000 0.000 0.092 0.016 0.892
#> GSM153120 1 0.5805 0.5653 0.664 0.036 0.000 0.212 0.088
#> GSM153121 3 0.2497 0.7630 0.000 0.004 0.880 0.004 0.112
#> GSM153122 5 0.3772 0.6880 0.000 0.000 0.172 0.036 0.792
#> GSM153123 3 0.5528 0.1464 0.000 0.432 0.512 0.008 0.048
#> GSM153124 4 0.5129 0.7088 0.004 0.136 0.108 0.736 0.016
#> GSM153125 4 0.2228 0.8122 0.004 0.076 0.012 0.908 0.000
#> GSM153126 3 0.1285 0.7749 0.000 0.004 0.956 0.004 0.036
#> GSM153127 2 0.0451 0.8552 0.000 0.988 0.008 0.004 0.000
#> GSM153128 5 0.4407 0.6291 0.000 0.016 0.180 0.040 0.764
#> GSM153129 3 0.3404 0.7474 0.000 0.124 0.840 0.012 0.024
#> GSM153130 3 0.2179 0.7576 0.000 0.004 0.896 0.000 0.100
#> GSM153131 3 0.2783 0.7484 0.000 0.012 0.868 0.004 0.116
#> GSM153132 3 0.4535 0.6571 0.000 0.092 0.748 0.000 0.160
#> GSM153133 2 0.5952 0.3157 0.000 0.540 0.380 0.040 0.040
#> GSM153134 3 0.3160 0.6986 0.000 0.188 0.808 0.000 0.004
#> GSM153135 2 0.0566 0.8550 0.000 0.984 0.012 0.004 0.000
#> GSM153136 4 0.2693 0.8151 0.060 0.028 0.000 0.896 0.016
#> GSM153137 2 0.2464 0.8242 0.000 0.904 0.004 0.044 0.048
#> GSM153138 2 0.5376 0.5960 0.000 0.672 0.016 0.072 0.240
#> GSM153139 3 0.2286 0.7533 0.000 0.004 0.888 0.000 0.108
#> GSM153140 2 0.5682 0.6528 0.000 0.656 0.172 0.164 0.008
#> GSM153141 2 0.0451 0.8550 0.000 0.988 0.008 0.004 0.000
#> GSM153142 5 0.2813 0.7414 0.000 0.000 0.168 0.000 0.832
#> GSM153143 2 0.2758 0.8185 0.000 0.888 0.012 0.076 0.024
#> GSM153144 3 0.4383 0.1977 0.000 0.424 0.572 0.004 0.000
#> GSM153145 5 0.2813 0.7414 0.000 0.000 0.168 0.000 0.832
#> GSM153146 2 0.1211 0.8537 0.000 0.960 0.024 0.000 0.016
#> GSM153147 3 0.3385 0.7579 0.000 0.084 0.856 0.016 0.044
#> GSM153148 2 0.0451 0.8552 0.000 0.988 0.008 0.004 0.000
#> GSM153149 2 0.4435 0.7506 0.000 0.768 0.164 0.012 0.056
#> GSM153150 4 0.6450 0.1726 0.392 0.024 0.000 0.484 0.100
#> GSM153151 5 0.7796 0.0124 0.000 0.184 0.352 0.084 0.380
#> GSM153152 3 0.4577 0.5392 0.000 0.296 0.676 0.004 0.024
#> GSM153153 2 0.2796 0.8207 0.000 0.868 0.116 0.008 0.008
#> GSM153154 3 0.3391 0.6747 0.000 0.012 0.800 0.000 0.188
#> GSM153155 2 0.4969 0.7374 0.000 0.732 0.188 0.036 0.044
#> GSM153156 3 0.2865 0.7455 0.000 0.004 0.856 0.008 0.132
#> GSM153157 5 0.2970 0.7417 0.000 0.000 0.168 0.004 0.828
#> GSM153158 5 0.4716 0.5937 0.000 0.036 0.308 0.000 0.656
#> GSM153159 5 0.3177 0.7247 0.000 0.000 0.208 0.000 0.792
#> GSM153160 3 0.1928 0.7687 0.000 0.004 0.920 0.004 0.072
#> GSM153161 2 0.1267 0.8477 0.000 0.960 0.004 0.012 0.024
#> GSM153162 3 0.1924 0.7692 0.000 0.064 0.924 0.004 0.008
#> GSM153163 3 0.1638 0.7727 0.000 0.004 0.932 0.000 0.064
#> GSM153164 5 0.6389 0.4624 0.000 0.136 0.300 0.016 0.548
#> GSM153165 3 0.1168 0.7780 0.000 0.008 0.960 0.000 0.032
#> GSM153166 3 0.4561 -0.0531 0.000 0.488 0.504 0.000 0.008
#> GSM153167 3 0.3799 0.7108 0.000 0.144 0.812 0.032 0.012
#> GSM153168 5 0.2813 0.7414 0.000 0.000 0.168 0.000 0.832
#> GSM153169 3 0.3211 0.7001 0.000 0.004 0.824 0.008 0.164
#> GSM153170 3 0.1386 0.7801 0.000 0.016 0.952 0.000 0.032
#> GSM153171 4 0.4449 0.7541 0.156 0.028 0.004 0.780 0.032
#> GSM153172 2 0.3353 0.7665 0.000 0.796 0.196 0.008 0.000
#> GSM153173 3 0.1518 0.7746 0.000 0.004 0.944 0.004 0.048
#> GSM153174 3 0.3706 0.6974 0.000 0.180 0.796 0.012 0.012
#> GSM153175 4 0.2674 0.7702 0.000 0.004 0.140 0.856 0.000
#> GSM153176 4 0.6269 0.5940 0.056 0.000 0.204 0.636 0.104
#> GSM153177 2 0.5032 0.1703 0.000 0.520 0.448 0.000 0.032
#> GSM152931 4 0.2266 0.8151 0.008 0.064 0.016 0.912 0.000
#> GSM152932 2 0.4262 0.6886 0.000 0.724 0.252 0.008 0.016
#> GSM152933 2 0.5053 0.6105 0.000 0.668 0.268 0.004 0.060
#> GSM152934 5 0.8598 -0.0304 0.144 0.104 0.044 0.320 0.388
#> GSM152935 5 0.3702 0.7136 0.000 0.032 0.092 0.036 0.840
#> GSM152936 4 0.3598 0.7817 0.012 0.072 0.008 0.852 0.056
#> GSM152937 5 0.5543 0.5448 0.016 0.020 0.208 0.060 0.696
#> GSM152938 3 0.5638 0.3458 0.000 0.020 0.580 0.048 0.352
#> GSM152939 4 0.3884 0.5913 0.000 0.004 0.288 0.708 0.000
#> GSM152940 1 0.6107 0.1435 0.508 0.024 0.000 0.400 0.068
#> GSM152941 1 0.0992 0.9029 0.968 0.000 0.000 0.024 0.008
#> GSM152942 3 0.1845 0.7629 0.000 0.000 0.928 0.056 0.016
#> GSM152943 5 0.8541 0.0770 0.156 0.252 0.008 0.216 0.368
#> GSM152944 3 0.2304 0.7606 0.000 0.008 0.892 0.000 0.100
#> GSM152945 5 0.2943 0.6736 0.004 0.028 0.012 0.072 0.884
#> GSM152946 2 0.6606 0.5215 0.000 0.584 0.208 0.172 0.036
#> GSM152947 1 0.5925 0.2380 0.528 0.012 0.000 0.384 0.076
#> GSM152948 2 0.0324 0.8553 0.000 0.992 0.004 0.004 0.000
#> GSM152949 3 0.1173 0.7793 0.000 0.020 0.964 0.004 0.012
#> GSM152950 3 0.5187 0.6643 0.000 0.132 0.716 0.012 0.140
#> GSM152951 2 0.1117 0.8556 0.000 0.964 0.020 0.016 0.000
#> GSM152952 2 0.0898 0.8512 0.000 0.972 0.000 0.020 0.008
#> GSM152953 2 0.1299 0.8510 0.000 0.960 0.008 0.012 0.020
#> GSM152954 4 0.2180 0.8162 0.032 0.020 0.000 0.924 0.024
#> GSM152955 5 0.2283 0.7154 0.000 0.008 0.040 0.036 0.916
#> GSM152956 2 0.0451 0.8552 0.000 0.988 0.008 0.004 0.000
#> GSM152957 4 0.4602 0.4938 0.340 0.000 0.004 0.640 0.016
#> GSM152958 4 0.3183 0.7997 0.108 0.028 0.000 0.856 0.008
#> GSM152959 1 0.4746 -0.0246 0.504 0.000 0.000 0.480 0.016
#> GSM152960 4 0.7159 0.5857 0.148 0.200 0.008 0.572 0.072
#> GSM152961 4 0.3095 0.8041 0.092 0.024 0.000 0.868 0.016
#> GSM152962 5 0.6478 0.2507 0.000 0.076 0.364 0.044 0.516
#> GSM152963 2 0.0693 0.8518 0.000 0.980 0.000 0.012 0.008
#> GSM152964 5 0.1818 0.7007 0.000 0.000 0.024 0.044 0.932
#> GSM152965 2 0.4777 0.6994 0.000 0.748 0.028 0.048 0.176
#> GSM152966 4 0.1959 0.8114 0.004 0.064 0.004 0.924 0.004
#> GSM152967 2 0.4184 0.7512 0.000 0.764 0.192 0.040 0.004
#> GSM152968 3 0.1653 0.7817 0.000 0.024 0.944 0.004 0.028
#> GSM152969 4 0.1894 0.8107 0.000 0.072 0.000 0.920 0.008
#> GSM152970 1 0.5098 0.4832 0.644 0.000 0.004 0.300 0.052
#> GSM152971 4 0.1918 0.8176 0.036 0.036 0.000 0.928 0.000
#> GSM152972 4 0.1970 0.8157 0.012 0.060 0.000 0.924 0.004
#> GSM152973 3 0.4196 0.3533 0.000 0.000 0.640 0.356 0.004
#> GSM152974 2 0.3395 0.7150 0.000 0.764 0.236 0.000 0.000
#> GSM152975 5 0.8214 0.2652 0.000 0.260 0.128 0.236 0.376
#> GSM152976 4 0.2860 0.8111 0.044 0.008 0.036 0.896 0.016
#> GSM152977 4 0.2650 0.7987 0.036 0.000 0.004 0.892 0.068
#> GSM152978 4 0.4071 0.7872 0.052 0.104 0.000 0.816 0.028
#> GSM152979 3 0.2787 0.7319 0.000 0.004 0.856 0.004 0.136
#> GSM152980 4 0.7899 0.1346 0.000 0.304 0.180 0.412 0.104
#> GSM152981 5 0.2848 0.7436 0.000 0.000 0.156 0.004 0.840
#> GSM152982 4 0.2859 0.7838 0.000 0.012 0.096 0.876 0.016
#> GSM152983 4 0.1996 0.8174 0.016 0.040 0.004 0.932 0.008
#> GSM152984 3 0.3300 0.7324 0.000 0.024 0.856 0.100 0.020
#> GSM152985 4 0.4561 0.0287 0.488 0.000 0.000 0.504 0.008
#> GSM152986 4 0.2157 0.8178 0.036 0.040 0.000 0.920 0.004
#> GSM152987 1 0.2152 0.8657 0.920 0.004 0.000 0.032 0.044
#> GSM152988 4 0.4350 0.3487 0.000 0.004 0.408 0.588 0.000
#> GSM152989 1 0.4470 0.3418 0.616 0.000 0.000 0.372 0.012
#> GSM152990 3 0.1205 0.7761 0.000 0.000 0.956 0.004 0.040
#> GSM152991 5 0.4892 0.6898 0.000 0.108 0.148 0.008 0.736
#> GSM187524 1 0.0451 0.9164 0.988 0.000 0.000 0.004 0.008
#> GSM187525 1 0.0451 0.9171 0.988 0.000 0.000 0.008 0.004
#> GSM187526 1 0.0290 0.9186 0.992 0.000 0.000 0.008 0.000
#> GSM187527 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152856 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152857 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152858 1 0.0290 0.9186 0.992 0.000 0.000 0.008 0.000
#> GSM152859 1 0.0451 0.9164 0.988 0.000 0.000 0.004 0.008
#> GSM152860 1 0.0162 0.9193 0.996 0.000 0.000 0.004 0.000
#> GSM152861 1 0.0162 0.9193 0.996 0.000 0.000 0.004 0.000
#> GSM152862 1 0.0290 0.9186 0.992 0.000 0.000 0.008 0.000
#> GSM152863 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152864 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152866 1 0.0162 0.9193 0.996 0.000 0.000 0.004 0.000
#> GSM152867 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152868 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152870 1 0.0290 0.9186 0.992 0.000 0.000 0.008 0.000
#> GSM152871 1 0.0290 0.9186 0.992 0.000 0.000 0.008 0.000
#> GSM152872 1 0.0290 0.9186 0.992 0.000 0.000 0.008 0.000
#> GSM152873 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152875 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152876 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152877 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152878 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152879 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.9202 1.000 0.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.6089 0.5962 0.000 0.628 0.172 0.040 0.028 0.132
#> GSM152805 5 0.3062 0.6254 0.000 0.000 0.160 0.000 0.816 0.024
#> GSM152806 5 0.1584 0.6796 0.000 0.000 0.064 0.000 0.928 0.008
#> GSM152807 2 0.1138 0.7629 0.000 0.960 0.004 0.012 0.000 0.024
#> GSM152808 5 0.1387 0.6803 0.000 0.000 0.068 0.000 0.932 0.000
#> GSM152809 2 0.1245 0.7619 0.000 0.952 0.000 0.016 0.000 0.032
#> GSM152810 5 0.4841 0.2940 0.100 0.000 0.000 0.004 0.660 0.236
#> GSM152811 5 0.2513 0.6735 0.000 0.000 0.060 0.008 0.888 0.044
#> GSM152812 2 0.1010 0.7584 0.000 0.960 0.000 0.004 0.000 0.036
#> GSM152813 2 0.2896 0.7507 0.000 0.864 0.080 0.012 0.000 0.044
#> GSM152814 2 0.2393 0.7538 0.000 0.892 0.040 0.004 0.000 0.064
#> GSM152815 2 0.0891 0.7612 0.000 0.968 0.008 0.000 0.000 0.024
#> GSM152816 3 0.6689 0.4545 0.000 0.092 0.556 0.012 0.192 0.148
#> GSM152817 5 0.1327 0.6805 0.000 0.000 0.064 0.000 0.936 0.000
#> GSM152818 5 0.1838 0.6797 0.000 0.000 0.068 0.000 0.916 0.016
#> GSM152819 5 0.6813 0.2663 0.000 0.248 0.120 0.004 0.508 0.120
#> GSM152820 5 0.7835 0.1221 0.000 0.140 0.220 0.028 0.400 0.212
#> GSM152821 2 0.1950 0.7644 0.000 0.912 0.024 0.000 0.000 0.064
#> GSM153115 4 0.1806 0.6906 0.000 0.020 0.008 0.928 0.000 0.044
#> GSM153116 5 0.2257 0.6780 0.000 0.016 0.060 0.000 0.904 0.020
#> GSM153117 5 0.6518 0.3205 0.000 0.212 0.172 0.000 0.536 0.080
#> GSM153118 2 0.4295 0.7186 0.000 0.776 0.096 0.000 0.048 0.080
#> GSM153119 5 0.3432 0.5757 0.000 0.000 0.052 0.000 0.800 0.148
#> GSM153120 1 0.7048 0.1093 0.448 0.048 0.000 0.160 0.028 0.316
#> GSM153121 3 0.3244 0.7222 0.000 0.004 0.832 0.000 0.064 0.100
#> GSM153122 5 0.5047 0.3193 0.000 0.000 0.136 0.000 0.628 0.236
#> GSM153123 3 0.6317 0.2675 0.000 0.288 0.492 0.000 0.032 0.188
#> GSM153124 4 0.6231 0.4247 0.000 0.132 0.152 0.596 0.000 0.120
#> GSM153125 4 0.1401 0.6930 0.000 0.028 0.000 0.948 0.004 0.020
#> GSM153126 3 0.1844 0.7398 0.000 0.000 0.924 0.004 0.048 0.024
#> GSM153127 2 0.1194 0.7612 0.000 0.956 0.004 0.008 0.000 0.032
#> GSM153128 5 0.5922 -0.1685 0.008 0.016 0.104 0.000 0.472 0.400
#> GSM153129 3 0.4612 0.6895 0.000 0.096 0.764 0.012 0.040 0.088
#> GSM153130 3 0.2662 0.7294 0.000 0.000 0.856 0.000 0.120 0.024
#> GSM153131 3 0.4628 0.6758 0.000 0.036 0.740 0.000 0.132 0.092
#> GSM153132 3 0.6713 0.4253 0.000 0.080 0.516 0.004 0.236 0.164
#> GSM153133 2 0.7164 0.1651 0.000 0.412 0.300 0.020 0.048 0.220
#> GSM153134 3 0.4030 0.6587 0.000 0.148 0.780 0.008 0.012 0.052
#> GSM153135 2 0.1075 0.7632 0.000 0.952 0.000 0.000 0.000 0.048
#> GSM153136 4 0.2883 0.6963 0.028 0.024 0.000 0.880 0.012 0.056
#> GSM153137 2 0.3290 0.6624 0.000 0.776 0.000 0.016 0.000 0.208
#> GSM153138 2 0.6420 0.1182 0.000 0.464 0.008 0.040 0.124 0.364
#> GSM153139 3 0.2942 0.7251 0.000 0.000 0.836 0.000 0.132 0.032
#> GSM153140 2 0.6776 0.5254 0.000 0.564 0.132 0.136 0.016 0.152
#> GSM153141 2 0.1531 0.7554 0.000 0.928 0.000 0.004 0.000 0.068
#> GSM153142 5 0.1951 0.6807 0.000 0.000 0.076 0.000 0.908 0.016
#> GSM153143 2 0.3308 0.7249 0.000 0.828 0.004 0.072 0.000 0.096
#> GSM153144 3 0.5543 0.2799 0.000 0.348 0.548 0.016 0.004 0.084
#> GSM153145 5 0.1643 0.6815 0.000 0.000 0.068 0.000 0.924 0.008
#> GSM153146 2 0.2226 0.7622 0.000 0.904 0.028 0.000 0.008 0.060
#> GSM153147 3 0.4190 0.7049 0.000 0.048 0.800 0.020 0.040 0.092
#> GSM153148 2 0.1477 0.7640 0.000 0.940 0.008 0.004 0.000 0.048
#> GSM153149 2 0.5228 0.6234 0.000 0.676 0.144 0.000 0.032 0.148
#> GSM153150 4 0.7143 0.0594 0.248 0.032 0.000 0.356 0.024 0.340
#> GSM153151 6 0.7458 0.5456 0.000 0.136 0.220 0.020 0.164 0.460
#> GSM153152 3 0.5976 0.4975 0.000 0.240 0.604 0.012 0.048 0.096
#> GSM153153 2 0.3140 0.7464 0.000 0.852 0.064 0.004 0.008 0.072
#> GSM153154 3 0.5342 0.5390 0.000 0.020 0.632 0.004 0.252 0.092
#> GSM153155 2 0.6261 0.5930 0.000 0.612 0.140 0.052 0.024 0.172
#> GSM153156 3 0.3920 0.6940 0.000 0.000 0.768 0.000 0.120 0.112
#> GSM153157 5 0.2987 0.6624 0.000 0.000 0.080 0.008 0.856 0.056
#> GSM153158 5 0.4852 0.5551 0.000 0.064 0.184 0.000 0.708 0.044
#> GSM153159 5 0.2831 0.6479 0.000 0.000 0.136 0.000 0.840 0.024
#> GSM153160 3 0.2201 0.7360 0.000 0.000 0.896 0.000 0.076 0.028
#> GSM153161 2 0.2588 0.7264 0.000 0.860 0.000 0.012 0.004 0.124
#> GSM153162 3 0.2258 0.7374 0.000 0.028 0.912 0.008 0.012 0.040
#> GSM153163 3 0.2170 0.7405 0.000 0.000 0.888 0.000 0.100 0.012
#> GSM153164 5 0.6666 0.3788 0.000 0.136 0.144 0.012 0.572 0.136
#> GSM153165 3 0.1074 0.7455 0.000 0.000 0.960 0.000 0.028 0.012
#> GSM153166 2 0.5809 0.2184 0.000 0.480 0.400 0.012 0.008 0.100
#> GSM153167 3 0.6251 0.5054 0.000 0.172 0.608 0.052 0.020 0.148
#> GSM153168 5 0.1398 0.6781 0.000 0.000 0.052 0.000 0.940 0.008
#> GSM153169 3 0.3727 0.6681 0.000 0.000 0.748 0.000 0.216 0.036
#> GSM153170 3 0.1860 0.7492 0.000 0.004 0.928 0.004 0.036 0.028
#> GSM153171 4 0.4985 0.5794 0.152 0.004 0.008 0.684 0.000 0.152
#> GSM153172 2 0.3883 0.7087 0.000 0.768 0.144 0.000 0.000 0.088
#> GSM153173 3 0.1524 0.7443 0.000 0.000 0.932 0.000 0.060 0.008
#> GSM153174 3 0.3881 0.6838 0.000 0.096 0.808 0.028 0.004 0.064
#> GSM153175 4 0.3419 0.6353 0.000 0.008 0.116 0.820 0.000 0.056
#> GSM153176 4 0.6360 0.4047 0.012 0.000 0.232 0.576 0.072 0.108
#> GSM153177 2 0.6478 0.3264 0.000 0.472 0.328 0.004 0.040 0.156
#> GSM152931 4 0.1237 0.6937 0.000 0.020 0.004 0.956 0.000 0.020
#> GSM152932 2 0.5514 0.5344 0.000 0.588 0.256 0.004 0.004 0.148
#> GSM152933 2 0.5849 0.5915 0.000 0.628 0.180 0.000 0.080 0.112
#> GSM152934 6 0.7254 0.5158 0.088 0.052 0.036 0.140 0.096 0.588
#> GSM152935 5 0.5528 0.3313 0.000 0.036 0.100 0.000 0.620 0.244
#> GSM152936 4 0.4447 0.5387 0.008 0.036 0.004 0.680 0.000 0.272
#> GSM152937 6 0.6062 0.4068 0.004 0.012 0.128 0.008 0.336 0.512
#> GSM152938 3 0.6418 -0.2525 0.000 0.012 0.428 0.016 0.168 0.376
#> GSM152939 4 0.4532 0.4285 0.000 0.008 0.292 0.656 0.000 0.044
#> GSM152940 4 0.6764 0.0997 0.312 0.008 0.000 0.332 0.020 0.328
#> GSM152941 1 0.2575 0.8440 0.872 0.000 0.000 0.024 0.004 0.100
#> GSM152942 3 0.3299 0.7088 0.000 0.000 0.844 0.080 0.028 0.048
#> GSM152943 6 0.6340 0.5550 0.076 0.144 0.000 0.052 0.092 0.636
#> GSM152944 3 0.3630 0.6967 0.000 0.004 0.780 0.000 0.176 0.040
#> GSM152945 5 0.5057 -0.2054 0.004 0.028 0.008 0.008 0.480 0.472
#> GSM152946 2 0.7452 0.1830 0.000 0.424 0.176 0.148 0.008 0.244
#> GSM152947 1 0.6447 -0.1620 0.364 0.004 0.000 0.304 0.008 0.320
#> GSM152948 2 0.1957 0.7647 0.000 0.920 0.008 0.024 0.000 0.048
#> GSM152949 3 0.2258 0.7424 0.000 0.008 0.908 0.008 0.020 0.056
#> GSM152950 3 0.6523 0.4747 0.000 0.152 0.588 0.012 0.116 0.132
#> GSM152951 2 0.2553 0.7570 0.000 0.888 0.012 0.044 0.000 0.056
#> GSM152952 2 0.2009 0.7494 0.000 0.904 0.004 0.008 0.000 0.084
#> GSM152953 2 0.2913 0.7196 0.000 0.812 0.004 0.004 0.000 0.180
#> GSM152954 4 0.3100 0.6844 0.012 0.008 0.000 0.844 0.016 0.120
#> GSM152955 5 0.3402 0.5648 0.000 0.000 0.020 0.012 0.800 0.168
#> GSM152956 2 0.0935 0.7626 0.000 0.964 0.004 0.000 0.000 0.032
#> GSM152957 4 0.5267 0.4504 0.292 0.000 0.004 0.588 0.000 0.116
#> GSM152958 4 0.3282 0.6722 0.092 0.008 0.000 0.840 0.004 0.056
#> GSM152959 4 0.5892 0.1616 0.416 0.000 0.000 0.432 0.012 0.140
#> GSM152960 4 0.7374 0.1829 0.096 0.136 0.004 0.436 0.020 0.308
#> GSM152961 4 0.3669 0.6565 0.104 0.000 0.000 0.804 0.008 0.084
#> GSM152962 6 0.7478 0.4133 0.000 0.076 0.264 0.016 0.288 0.356
#> GSM152963 2 0.1714 0.7495 0.000 0.908 0.000 0.000 0.000 0.092
#> GSM152964 5 0.3575 0.3725 0.000 0.000 0.008 0.000 0.708 0.284
#> GSM152965 2 0.5845 0.2694 0.000 0.536 0.024 0.004 0.104 0.332
#> GSM152966 4 0.1377 0.6938 0.000 0.016 0.004 0.952 0.004 0.024
#> GSM152967 2 0.5907 0.5748 0.000 0.624 0.212 0.068 0.008 0.088
#> GSM152968 3 0.2664 0.7455 0.000 0.032 0.888 0.004 0.020 0.056
#> GSM152969 4 0.1296 0.6937 0.000 0.012 0.000 0.952 0.004 0.032
#> GSM152970 1 0.5229 0.4103 0.604 0.000 0.000 0.240 0.000 0.156
#> GSM152971 4 0.0862 0.6940 0.000 0.008 0.000 0.972 0.004 0.016
#> GSM152972 4 0.1769 0.6947 0.004 0.012 0.000 0.924 0.000 0.060
#> GSM152973 3 0.4411 0.4479 0.000 0.004 0.672 0.276 0.000 0.048
#> GSM152974 2 0.4594 0.6290 0.000 0.700 0.216 0.012 0.000 0.072
#> GSM152975 5 0.8553 -0.1591 0.000 0.220 0.104 0.216 0.328 0.132
#> GSM152976 4 0.3660 0.6833 0.044 0.004 0.020 0.836 0.016 0.080
#> GSM152977 4 0.4333 0.6005 0.000 0.000 0.008 0.744 0.124 0.124
#> GSM152978 4 0.5108 0.5838 0.016 0.100 0.004 0.704 0.012 0.164
#> GSM152979 3 0.2980 0.6988 0.000 0.000 0.808 0.000 0.180 0.012
#> GSM152980 4 0.8571 -0.1689 0.000 0.248 0.112 0.272 0.108 0.260
#> GSM152981 5 0.1391 0.6738 0.000 0.000 0.040 0.000 0.944 0.016
#> GSM152982 4 0.3246 0.6708 0.004 0.000 0.060 0.852 0.020 0.064
#> GSM152983 4 0.2128 0.6950 0.004 0.008 0.004 0.912 0.008 0.064
#> GSM152984 3 0.4002 0.6776 0.000 0.012 0.804 0.100 0.024 0.060
#> GSM152985 4 0.5695 0.2126 0.416 0.000 0.000 0.460 0.012 0.112
#> GSM152986 4 0.1448 0.6961 0.016 0.012 0.000 0.948 0.000 0.024
#> GSM152987 1 0.3833 0.6398 0.708 0.000 0.000 0.004 0.016 0.272
#> GSM152988 4 0.4723 0.2366 0.000 0.004 0.408 0.548 0.000 0.040
#> GSM152989 1 0.5269 0.1870 0.548 0.000 0.000 0.360 0.008 0.084
#> GSM152990 3 0.2058 0.7482 0.000 0.000 0.908 0.000 0.056 0.036
#> GSM152991 5 0.5344 0.5159 0.000 0.076 0.080 0.008 0.700 0.136
#> GSM187524 1 0.1524 0.8859 0.932 0.000 0.000 0.000 0.008 0.060
#> GSM187525 1 0.1285 0.8891 0.944 0.000 0.000 0.000 0.004 0.052
#> GSM187526 1 0.1082 0.8948 0.956 0.000 0.000 0.000 0.004 0.040
#> GSM187527 1 0.1124 0.8984 0.956 0.000 0.000 0.000 0.008 0.036
#> GSM152856 1 0.1124 0.8984 0.956 0.000 0.000 0.000 0.008 0.036
#> GSM152857 1 0.1124 0.8984 0.956 0.000 0.000 0.000 0.008 0.036
#> GSM152858 1 0.0777 0.8978 0.972 0.000 0.000 0.000 0.004 0.024
#> GSM152859 1 0.0935 0.8957 0.964 0.000 0.000 0.000 0.004 0.032
#> GSM152860 1 0.0777 0.8978 0.972 0.000 0.000 0.000 0.004 0.024
#> GSM152861 1 0.0260 0.9012 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM152862 1 0.0777 0.8978 0.972 0.000 0.000 0.000 0.004 0.024
#> GSM152863 1 0.0146 0.9014 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM152864 1 0.0000 0.9015 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152865 1 0.0260 0.9011 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM152866 1 0.1152 0.8997 0.952 0.000 0.000 0.000 0.004 0.044
#> GSM152867 1 0.0000 0.9015 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152868 1 0.0000 0.9015 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.9015 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152870 1 0.0777 0.8978 0.972 0.000 0.000 0.000 0.004 0.024
#> GSM152871 1 0.0692 0.8987 0.976 0.000 0.000 0.000 0.004 0.020
#> GSM152872 1 0.0777 0.8978 0.972 0.000 0.000 0.000 0.004 0.024
#> GSM152873 1 0.1124 0.8984 0.956 0.000 0.000 0.000 0.008 0.036
#> GSM152874 1 0.1124 0.8984 0.956 0.000 0.000 0.000 0.008 0.036
#> GSM152875 1 0.1124 0.8984 0.956 0.000 0.000 0.000 0.008 0.036
#> GSM152876 1 0.1124 0.8984 0.956 0.000 0.000 0.000 0.008 0.036
#> GSM152877 1 0.1124 0.8984 0.956 0.000 0.000 0.000 0.008 0.036
#> GSM152878 1 0.1124 0.8984 0.956 0.000 0.000 0.000 0.008 0.036
#> GSM152879 1 0.1124 0.8984 0.956 0.000 0.000 0.000 0.008 0.036
#> GSM152880 1 0.1124 0.8984 0.956 0.000 0.000 0.000 0.008 0.036
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> CV:skmeans 170 2.13e-14 2
#> CV:skmeans 151 1.57e-14 3
#> CV:skmeans 152 1.75e-21 4
#> CV:skmeans 145 8.03e-24 5
#> CV:skmeans 129 1.90e-22 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "pam"]
# you can also extract it by
# res = res_list["CV:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.709 0.922 0.945 0.3271 0.694 0.694
#> 3 3 0.426 0.757 0.823 0.7894 0.701 0.575
#> 4 4 0.512 0.738 0.808 0.1192 0.951 0.886
#> 5 5 0.525 0.647 0.797 0.0771 0.888 0.719
#> 6 6 0.598 0.561 0.780 0.0460 0.953 0.846
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.4298 0.9325 0.088 0.912
#> GSM152805 2 0.0000 0.9407 0.000 1.000
#> GSM152806 2 0.0000 0.9407 0.000 1.000
#> GSM152807 2 0.3431 0.9396 0.064 0.936
#> GSM152808 2 0.0376 0.9419 0.004 0.996
#> GSM152809 2 0.6048 0.9022 0.148 0.852
#> GSM152810 2 0.4022 0.9332 0.080 0.920
#> GSM152811 2 0.0000 0.9407 0.000 1.000
#> GSM152812 2 0.2603 0.9418 0.044 0.956
#> GSM152813 2 0.2778 0.9420 0.048 0.952
#> GSM152814 2 0.0000 0.9407 0.000 1.000
#> GSM152815 2 0.2603 0.9418 0.044 0.956
#> GSM152816 2 0.0000 0.9407 0.000 1.000
#> GSM152817 2 0.0000 0.9407 0.000 1.000
#> GSM152818 2 0.0376 0.9419 0.004 0.996
#> GSM152819 2 0.2043 0.9433 0.032 0.968
#> GSM152820 2 0.2603 0.9418 0.044 0.956
#> GSM152821 2 0.0938 0.9433 0.012 0.988
#> GSM153115 2 0.6048 0.9022 0.148 0.852
#> GSM153116 2 0.0000 0.9407 0.000 1.000
#> GSM153117 2 0.0000 0.9407 0.000 1.000
#> GSM153118 2 0.0376 0.9419 0.004 0.996
#> GSM153119 2 0.0000 0.9407 0.000 1.000
#> GSM153120 2 0.6438 0.8884 0.164 0.836
#> GSM153121 2 0.1184 0.9424 0.016 0.984
#> GSM153122 2 0.0000 0.9407 0.000 1.000
#> GSM153123 2 0.0376 0.9420 0.004 0.996
#> GSM153124 2 0.4161 0.9346 0.084 0.916
#> GSM153125 2 0.6048 0.9022 0.148 0.852
#> GSM153126 2 0.3274 0.9368 0.060 0.940
#> GSM153127 2 0.3114 0.9409 0.056 0.944
#> GSM153128 2 0.0376 0.9419 0.004 0.996
#> GSM153129 2 0.1414 0.9447 0.020 0.980
#> GSM153130 2 0.0000 0.9407 0.000 1.000
#> GSM153131 2 0.0000 0.9407 0.000 1.000
#> GSM153132 2 0.1414 0.9436 0.020 0.980
#> GSM153133 2 0.3431 0.9409 0.064 0.936
#> GSM153134 2 0.0000 0.9407 0.000 1.000
#> GSM153135 2 0.3431 0.9401 0.064 0.936
#> GSM153136 2 0.6048 0.9022 0.148 0.852
#> GSM153137 2 0.3733 0.9379 0.072 0.928
#> GSM153138 2 0.2043 0.9435 0.032 0.968
#> GSM153139 2 0.0000 0.9407 0.000 1.000
#> GSM153140 2 0.3584 0.9392 0.068 0.932
#> GSM153141 2 0.2423 0.9425 0.040 0.960
#> GSM153142 2 0.0000 0.9407 0.000 1.000
#> GSM153143 2 0.5178 0.9201 0.116 0.884
#> GSM153144 2 0.1184 0.9424 0.016 0.984
#> GSM153145 2 0.0000 0.9407 0.000 1.000
#> GSM153146 2 0.0376 0.9419 0.004 0.996
#> GSM153147 2 0.3879 0.9329 0.076 0.924
#> GSM153148 2 0.2778 0.9419 0.048 0.952
#> GSM153149 2 0.0376 0.9419 0.004 0.996
#> GSM153150 2 0.5842 0.9074 0.140 0.860
#> GSM153151 2 0.1633 0.9445 0.024 0.976
#> GSM153152 2 0.0376 0.9419 0.004 0.996
#> GSM153153 2 0.0672 0.9428 0.008 0.992
#> GSM153154 2 0.2948 0.9395 0.052 0.948
#> GSM153155 2 0.4298 0.9328 0.088 0.912
#> GSM153156 2 0.0376 0.9418 0.004 0.996
#> GSM153157 2 0.0000 0.9407 0.000 1.000
#> GSM153158 2 0.0000 0.9407 0.000 1.000
#> GSM153159 2 0.0000 0.9407 0.000 1.000
#> GSM153160 2 0.2603 0.9407 0.044 0.956
#> GSM153161 2 0.2778 0.9418 0.048 0.952
#> GSM153162 2 0.0672 0.9419 0.008 0.992
#> GSM153163 2 0.0376 0.9416 0.004 0.996
#> GSM153164 2 0.1633 0.9437 0.024 0.976
#> GSM153165 2 0.0000 0.9407 0.000 1.000
#> GSM153166 2 0.0376 0.9419 0.004 0.996
#> GSM153167 2 0.0938 0.9432 0.012 0.988
#> GSM153168 2 0.0000 0.9407 0.000 1.000
#> GSM153169 2 0.0000 0.9407 0.000 1.000
#> GSM153170 2 0.0000 0.9407 0.000 1.000
#> GSM153171 2 0.6048 0.9022 0.148 0.852
#> GSM153172 2 0.0376 0.9419 0.004 0.996
#> GSM153173 2 0.0000 0.9407 0.000 1.000
#> GSM153174 2 0.3584 0.9389 0.068 0.932
#> GSM153175 2 0.5519 0.9149 0.128 0.872
#> GSM153176 2 0.6048 0.9022 0.148 0.852
#> GSM153177 2 0.0000 0.9407 0.000 1.000
#> GSM152931 2 0.6048 0.9022 0.148 0.852
#> GSM152932 2 0.0672 0.9427 0.008 0.992
#> GSM152933 2 0.0376 0.9419 0.004 0.996
#> GSM152934 2 0.6048 0.9022 0.148 0.852
#> GSM152935 2 0.0000 0.9407 0.000 1.000
#> GSM152936 2 0.5842 0.9078 0.140 0.860
#> GSM152937 2 0.0938 0.9436 0.012 0.988
#> GSM152938 2 0.0000 0.9407 0.000 1.000
#> GSM152939 2 0.6048 0.9022 0.148 0.852
#> GSM152940 2 0.6048 0.9022 0.148 0.852
#> GSM152941 1 0.3274 0.9056 0.940 0.060
#> GSM152942 2 0.4562 0.9267 0.096 0.904
#> GSM152943 2 0.5629 0.9117 0.132 0.868
#> GSM152944 2 0.0000 0.9407 0.000 1.000
#> GSM152945 2 0.1843 0.9450 0.028 0.972
#> GSM152946 2 0.4562 0.9298 0.096 0.904
#> GSM152947 2 0.6148 0.8993 0.152 0.848
#> GSM152948 2 0.1414 0.9439 0.020 0.980
#> GSM152949 2 0.2778 0.9402 0.048 0.952
#> GSM152950 2 0.0672 0.9426 0.008 0.992
#> GSM152951 2 0.5629 0.9120 0.132 0.868
#> GSM152952 2 0.3733 0.9380 0.072 0.928
#> GSM152953 2 0.2423 0.9425 0.040 0.960
#> GSM152954 2 0.6048 0.9022 0.148 0.852
#> GSM152955 2 0.2778 0.9426 0.048 0.952
#> GSM152956 2 0.2603 0.9426 0.044 0.956
#> GSM152957 2 0.6048 0.9022 0.148 0.852
#> GSM152958 2 0.6148 0.8990 0.152 0.848
#> GSM152959 2 0.6048 0.9022 0.148 0.852
#> GSM152960 2 0.6048 0.9022 0.148 0.852
#> GSM152961 2 0.6148 0.8990 0.152 0.848
#> GSM152962 2 0.0000 0.9407 0.000 1.000
#> GSM152963 2 0.4022 0.9354 0.080 0.920
#> GSM152964 2 0.3274 0.9366 0.060 0.940
#> GSM152965 2 0.1414 0.9443 0.020 0.980
#> GSM152966 2 0.6048 0.9022 0.148 0.852
#> GSM152967 2 0.4939 0.9237 0.108 0.892
#> GSM152968 2 0.0000 0.9407 0.000 1.000
#> GSM152969 2 0.6048 0.9022 0.148 0.852
#> GSM152970 2 0.5737 0.9111 0.136 0.864
#> GSM152971 2 0.6048 0.9022 0.148 0.852
#> GSM152972 2 0.6048 0.9022 0.148 0.852
#> GSM152973 2 0.5059 0.9168 0.112 0.888
#> GSM152974 2 0.0376 0.9419 0.004 0.996
#> GSM152975 2 0.5178 0.9204 0.116 0.884
#> GSM152976 2 0.5294 0.9186 0.120 0.880
#> GSM152977 2 0.5946 0.9050 0.144 0.856
#> GSM152978 2 0.6048 0.9022 0.148 0.852
#> GSM152979 2 0.0000 0.9407 0.000 1.000
#> GSM152980 2 0.3114 0.9414 0.056 0.944
#> GSM152981 2 0.0000 0.9407 0.000 1.000
#> GSM152982 2 0.5737 0.9099 0.136 0.864
#> GSM152983 2 0.6048 0.9022 0.148 0.852
#> GSM152984 2 0.4562 0.9258 0.096 0.904
#> GSM152985 1 0.9909 0.0516 0.556 0.444
#> GSM152986 2 0.6048 0.9022 0.148 0.852
#> GSM152987 1 0.4161 0.8867 0.916 0.084
#> GSM152988 2 0.5842 0.9065 0.140 0.860
#> GSM152989 2 0.8267 0.7646 0.260 0.740
#> GSM152990 2 0.0000 0.9407 0.000 1.000
#> GSM152991 2 0.0000 0.9407 0.000 1.000
#> GSM187524 1 0.0672 0.9520 0.992 0.008
#> GSM187525 1 0.0000 0.9568 1.000 0.000
#> GSM187526 1 0.0938 0.9492 0.988 0.012
#> GSM187527 1 0.3431 0.9009 0.936 0.064
#> GSM152856 1 0.0000 0.9568 1.000 0.000
#> GSM152857 1 0.9998 -0.0962 0.508 0.492
#> GSM152858 1 0.0000 0.9568 1.000 0.000
#> GSM152859 1 0.1633 0.9384 0.976 0.024
#> GSM152860 1 0.0000 0.9568 1.000 0.000
#> GSM152861 1 0.0000 0.9568 1.000 0.000
#> GSM152862 1 0.0376 0.9541 0.996 0.004
#> GSM152863 1 0.0000 0.9568 1.000 0.000
#> GSM152864 1 0.0000 0.9568 1.000 0.000
#> GSM152865 1 0.0000 0.9568 1.000 0.000
#> GSM152866 1 0.0000 0.9568 1.000 0.000
#> GSM152867 1 0.0000 0.9568 1.000 0.000
#> GSM152868 1 0.0000 0.9568 1.000 0.000
#> GSM152869 1 0.0000 0.9568 1.000 0.000
#> GSM152870 1 0.0000 0.9568 1.000 0.000
#> GSM152871 1 0.0000 0.9568 1.000 0.000
#> GSM152872 1 0.0000 0.9568 1.000 0.000
#> GSM152873 1 0.0000 0.9568 1.000 0.000
#> GSM152874 1 0.0000 0.9568 1.000 0.000
#> GSM152875 1 0.0000 0.9568 1.000 0.000
#> GSM152876 1 0.0000 0.9568 1.000 0.000
#> GSM152877 1 0.0000 0.9568 1.000 0.000
#> GSM152878 1 0.1414 0.9455 0.980 0.020
#> GSM152879 1 0.0000 0.9568 1.000 0.000
#> GSM152880 1 0.0000 0.9568 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 3 0.3267 0.7206 0.000 0.116 0.884
#> GSM152805 3 0.5431 0.7166 0.000 0.284 0.716
#> GSM152806 3 0.5431 0.7166 0.000 0.284 0.716
#> GSM152807 3 0.3816 0.6695 0.000 0.148 0.852
#> GSM152808 3 0.5529 0.7156 0.000 0.296 0.704
#> GSM152809 3 0.6140 -0.1897 0.000 0.404 0.596
#> GSM152810 2 0.6299 0.5581 0.000 0.524 0.476
#> GSM152811 3 0.4702 0.7654 0.000 0.212 0.788
#> GSM152812 3 0.2066 0.7632 0.000 0.060 0.940
#> GSM152813 3 0.2066 0.7644 0.000 0.060 0.940
#> GSM152814 3 0.0592 0.7961 0.000 0.012 0.988
#> GSM152815 3 0.2066 0.7632 0.000 0.060 0.940
#> GSM152816 3 0.2711 0.7930 0.000 0.088 0.912
#> GSM152817 3 0.5431 0.7166 0.000 0.284 0.716
#> GSM152818 3 0.5529 0.7152 0.000 0.296 0.704
#> GSM152819 3 0.5216 0.7478 0.000 0.260 0.740
#> GSM152820 3 0.4002 0.7924 0.000 0.160 0.840
#> GSM152821 3 0.1031 0.7934 0.000 0.024 0.976
#> GSM153115 2 0.5588 0.8516 0.004 0.720 0.276
#> GSM153116 3 0.4887 0.7435 0.000 0.228 0.772
#> GSM153117 3 0.4555 0.7513 0.000 0.200 0.800
#> GSM153118 3 0.3619 0.7802 0.000 0.136 0.864
#> GSM153119 3 0.5497 0.7145 0.000 0.292 0.708
#> GSM153120 2 0.5656 0.8482 0.008 0.728 0.264
#> GSM153121 3 0.5497 0.7289 0.000 0.292 0.708
#> GSM153122 3 0.5363 0.7333 0.000 0.276 0.724
#> GSM153123 3 0.0892 0.7969 0.000 0.020 0.980
#> GSM153124 3 0.3851 0.6869 0.004 0.136 0.860
#> GSM153125 2 0.6386 0.7160 0.004 0.584 0.412
#> GSM153126 2 0.6033 0.6806 0.004 0.660 0.336
#> GSM153127 3 0.2711 0.7614 0.000 0.088 0.912
#> GSM153128 3 0.2261 0.8044 0.000 0.068 0.932
#> GSM153129 3 0.3340 0.7933 0.000 0.120 0.880
#> GSM153130 3 0.4605 0.7670 0.000 0.204 0.796
#> GSM153131 3 0.3482 0.7866 0.000 0.128 0.872
#> GSM153132 3 0.3192 0.7999 0.000 0.112 0.888
#> GSM153133 3 0.2878 0.7439 0.000 0.096 0.904
#> GSM153134 3 0.1411 0.7982 0.000 0.036 0.964
#> GSM153135 3 0.2711 0.7447 0.000 0.088 0.912
#> GSM153136 2 0.5443 0.8478 0.004 0.736 0.260
#> GSM153137 3 0.2625 0.7480 0.000 0.084 0.916
#> GSM153138 3 0.1289 0.7798 0.000 0.032 0.968
#> GSM153139 3 0.2796 0.7916 0.000 0.092 0.908
#> GSM153140 3 0.3112 0.7326 0.004 0.096 0.900
#> GSM153141 3 0.1860 0.7689 0.000 0.052 0.948
#> GSM153142 3 0.5254 0.7282 0.000 0.264 0.736
#> GSM153143 3 0.5621 0.6612 0.000 0.308 0.692
#> GSM153144 3 0.4883 0.5285 0.004 0.208 0.788
#> GSM153145 3 0.5431 0.7166 0.000 0.284 0.716
#> GSM153146 3 0.2448 0.8012 0.000 0.076 0.924
#> GSM153147 2 0.6460 0.6954 0.004 0.556 0.440
#> GSM153148 3 0.2066 0.7632 0.000 0.060 0.940
#> GSM153149 3 0.0892 0.7932 0.000 0.020 0.980
#> GSM153150 2 0.5785 0.8436 0.004 0.696 0.300
#> GSM153151 3 0.3030 0.7957 0.004 0.092 0.904
#> GSM153152 3 0.4605 0.6373 0.000 0.204 0.796
#> GSM153153 3 0.1031 0.7966 0.000 0.024 0.976
#> GSM153154 3 0.6244 0.5667 0.000 0.440 0.560
#> GSM153155 3 0.3116 0.7238 0.000 0.108 0.892
#> GSM153156 3 0.3267 0.7879 0.000 0.116 0.884
#> GSM153157 3 0.5465 0.7155 0.000 0.288 0.712
#> GSM153158 3 0.4702 0.7483 0.000 0.212 0.788
#> GSM153159 3 0.5497 0.7146 0.000 0.292 0.708
#> GSM153160 2 0.6209 0.6344 0.004 0.628 0.368
#> GSM153161 3 0.2356 0.7570 0.000 0.072 0.928
#> GSM153162 2 0.6274 0.6700 0.000 0.544 0.456
#> GSM153163 3 0.4062 0.7821 0.000 0.164 0.836
#> GSM153164 3 0.5016 0.7516 0.000 0.240 0.760
#> GSM153165 3 0.3038 0.7877 0.000 0.104 0.896
#> GSM153166 3 0.1031 0.7965 0.000 0.024 0.976
#> GSM153167 3 0.1289 0.7961 0.000 0.032 0.968
#> GSM153168 3 0.5397 0.7188 0.000 0.280 0.720
#> GSM153169 3 0.3116 0.7878 0.000 0.108 0.892
#> GSM153170 3 0.4452 0.7628 0.000 0.192 0.808
#> GSM153171 2 0.5690 0.8504 0.004 0.708 0.288
#> GSM153172 3 0.0237 0.7888 0.000 0.004 0.996
#> GSM153173 3 0.6026 0.6516 0.000 0.376 0.624
#> GSM153174 2 0.6104 0.7513 0.004 0.648 0.348
#> GSM153175 2 0.5656 0.8078 0.004 0.712 0.284
#> GSM153176 2 0.4465 0.8055 0.004 0.820 0.176
#> GSM153177 3 0.1163 0.7985 0.000 0.028 0.972
#> GSM152931 2 0.5623 0.8503 0.004 0.716 0.280
#> GSM152932 3 0.0892 0.7857 0.000 0.020 0.980
#> GSM152933 3 0.2448 0.8056 0.000 0.076 0.924
#> GSM152934 2 0.5656 0.8509 0.004 0.712 0.284
#> GSM152935 3 0.3267 0.7945 0.000 0.116 0.884
#> GSM152936 2 0.5815 0.8448 0.004 0.692 0.304
#> GSM152937 3 0.2796 0.8031 0.000 0.092 0.908
#> GSM152938 3 0.6008 0.2568 0.000 0.372 0.628
#> GSM152939 2 0.5480 0.8509 0.004 0.732 0.264
#> GSM152940 2 0.5623 0.8503 0.004 0.716 0.280
#> GSM152941 1 0.6306 0.6909 0.748 0.200 0.052
#> GSM152942 2 0.5553 0.7539 0.004 0.724 0.272
#> GSM152943 3 0.4733 0.5829 0.004 0.196 0.800
#> GSM152944 3 0.5397 0.7189 0.000 0.280 0.720
#> GSM152945 3 0.4702 0.7522 0.000 0.212 0.788
#> GSM152946 3 0.3500 0.7123 0.004 0.116 0.880
#> GSM152947 2 0.5517 0.8512 0.004 0.728 0.268
#> GSM152948 3 0.1031 0.7833 0.000 0.024 0.976
#> GSM152949 2 0.6247 0.1941 0.004 0.620 0.376
#> GSM152950 2 0.6235 0.1698 0.000 0.564 0.436
#> GSM152951 3 0.4784 0.5749 0.004 0.200 0.796
#> GSM152952 3 0.2625 0.7462 0.000 0.084 0.916
#> GSM152953 3 0.1860 0.7688 0.000 0.052 0.948
#> GSM152954 2 0.6345 0.7325 0.004 0.596 0.400
#> GSM152955 3 0.5178 0.7473 0.000 0.256 0.744
#> GSM152956 3 0.2066 0.7641 0.000 0.060 0.940
#> GSM152957 2 0.5553 0.8510 0.004 0.724 0.272
#> GSM152958 2 0.5623 0.8503 0.004 0.716 0.280
#> GSM152959 2 0.5623 0.8503 0.004 0.716 0.280
#> GSM152960 3 0.5845 0.2677 0.004 0.308 0.688
#> GSM152961 2 0.5728 0.8508 0.008 0.720 0.272
#> GSM152962 3 0.0892 0.7979 0.000 0.020 0.980
#> GSM152963 3 0.2711 0.7422 0.000 0.088 0.912
#> GSM152964 3 0.5785 0.7025 0.000 0.332 0.668
#> GSM152965 3 0.1031 0.7897 0.000 0.024 0.976
#> GSM152966 2 0.5623 0.8503 0.004 0.716 0.280
#> GSM152967 2 0.5926 0.8233 0.000 0.644 0.356
#> GSM152968 3 0.3340 0.7878 0.000 0.120 0.880
#> GSM152969 3 0.5201 0.5067 0.004 0.236 0.760
#> GSM152970 2 0.6427 0.8135 0.012 0.640 0.348
#> GSM152971 2 0.5623 0.8503 0.004 0.716 0.280
#> GSM152972 2 0.5623 0.8503 0.004 0.716 0.280
#> GSM152973 2 0.5070 0.7873 0.004 0.772 0.224
#> GSM152974 3 0.1031 0.7851 0.000 0.024 0.976
#> GSM152975 2 0.6410 0.6171 0.004 0.576 0.420
#> GSM152976 2 0.6104 0.8184 0.004 0.648 0.348
#> GSM152977 2 0.4931 0.8089 0.004 0.784 0.212
#> GSM152978 3 0.6330 -0.0741 0.004 0.396 0.600
#> GSM152979 3 0.4750 0.7606 0.000 0.216 0.784
#> GSM152980 3 0.2860 0.7623 0.004 0.084 0.912
#> GSM152981 3 0.5431 0.7166 0.000 0.284 0.716
#> GSM152982 2 0.5588 0.8356 0.004 0.720 0.276
#> GSM152983 2 0.5588 0.8501 0.004 0.720 0.276
#> GSM152984 2 0.6126 0.8002 0.004 0.644 0.352
#> GSM152985 2 0.7126 0.7512 0.116 0.720 0.164
#> GSM152986 2 0.5623 0.8503 0.004 0.716 0.280
#> GSM152987 1 0.6192 0.7320 0.764 0.176 0.060
#> GSM152988 2 0.5553 0.8492 0.004 0.724 0.272
#> GSM152989 2 0.6764 0.8227 0.060 0.716 0.224
#> GSM152990 3 0.3482 0.7823 0.000 0.128 0.872
#> GSM152991 3 0.4974 0.7413 0.000 0.236 0.764
#> GSM187524 1 0.2339 0.9183 0.940 0.048 0.012
#> GSM187525 1 0.1753 0.9258 0.952 0.048 0.000
#> GSM187526 1 0.3454 0.8693 0.888 0.104 0.008
#> GSM187527 2 0.7796 0.2400 0.392 0.552 0.056
#> GSM152856 1 0.0000 0.9476 1.000 0.000 0.000
#> GSM152857 2 0.8373 0.1138 0.388 0.524 0.088
#> GSM152858 1 0.0000 0.9476 1.000 0.000 0.000
#> GSM152859 1 0.0424 0.9462 0.992 0.008 0.000
#> GSM152860 1 0.0424 0.9462 0.992 0.008 0.000
#> GSM152861 1 0.0237 0.9469 0.996 0.004 0.000
#> GSM152862 1 0.0424 0.9462 0.992 0.008 0.000
#> GSM152863 1 0.0237 0.9471 0.996 0.004 0.000
#> GSM152864 1 0.0000 0.9476 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.9476 1.000 0.000 0.000
#> GSM152866 1 0.0237 0.9470 0.996 0.004 0.000
#> GSM152867 1 0.0000 0.9476 1.000 0.000 0.000
#> GSM152868 1 0.2165 0.9119 0.936 0.064 0.000
#> GSM152869 1 0.2878 0.8841 0.904 0.096 0.000
#> GSM152870 1 0.0747 0.9429 0.984 0.016 0.000
#> GSM152871 1 0.0000 0.9476 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.9476 1.000 0.000 0.000
#> GSM152873 1 0.0000 0.9476 1.000 0.000 0.000
#> GSM152874 1 0.0000 0.9476 1.000 0.000 0.000
#> GSM152875 1 0.0000 0.9476 1.000 0.000 0.000
#> GSM152876 1 0.5138 0.6768 0.748 0.252 0.000
#> GSM152877 1 0.0000 0.9476 1.000 0.000 0.000
#> GSM152878 1 0.5167 0.7500 0.792 0.192 0.016
#> GSM152879 1 0.0000 0.9476 1.000 0.000 0.000
#> GSM152880 1 0.0000 0.9476 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.2480 0.79111 0.000 0.904 0.008 0.088
#> GSM152805 2 0.4830 0.71148 0.000 0.608 0.392 0.000
#> GSM152806 2 0.4898 0.70294 0.000 0.584 0.416 0.000
#> GSM152807 2 0.2714 0.76732 0.000 0.884 0.004 0.112
#> GSM152808 2 0.5088 0.69691 0.000 0.572 0.424 0.004
#> GSM152809 2 0.5158 -0.00769 0.000 0.524 0.004 0.472
#> GSM152810 4 0.6278 0.38707 0.000 0.408 0.060 0.532
#> GSM152811 2 0.5326 0.76284 0.000 0.748 0.136 0.116
#> GSM152812 2 0.1004 0.80310 0.000 0.972 0.004 0.024
#> GSM152813 2 0.1635 0.80557 0.000 0.948 0.008 0.044
#> GSM152814 2 0.1284 0.80823 0.000 0.964 0.024 0.012
#> GSM152815 2 0.0817 0.80166 0.000 0.976 0.000 0.024
#> GSM152816 2 0.1637 0.80859 0.000 0.940 0.060 0.000
#> GSM152817 2 0.4916 0.69918 0.000 0.576 0.424 0.000
#> GSM152818 2 0.4916 0.69918 0.000 0.576 0.424 0.000
#> GSM152819 2 0.4509 0.75147 0.000 0.708 0.288 0.004
#> GSM152820 2 0.3354 0.80173 0.000 0.872 0.044 0.084
#> GSM152821 2 0.0779 0.80370 0.000 0.980 0.004 0.016
#> GSM153115 4 0.3266 0.76032 0.000 0.168 0.000 0.832
#> GSM153116 2 0.4917 0.72891 0.000 0.656 0.336 0.008
#> GSM153117 2 0.5204 0.72175 0.000 0.612 0.376 0.012
#> GSM153118 2 0.3428 0.80126 0.000 0.844 0.144 0.012
#> GSM153119 2 0.4916 0.69918 0.000 0.576 0.424 0.000
#> GSM153120 4 0.0336 0.81125 0.000 0.008 0.000 0.992
#> GSM153121 2 0.5326 0.71467 0.000 0.604 0.380 0.016
#> GSM153122 2 0.5907 0.74121 0.000 0.680 0.228 0.092
#> GSM153123 2 0.1767 0.80889 0.000 0.944 0.044 0.012
#> GSM153124 2 0.3610 0.71470 0.000 0.800 0.000 0.200
#> GSM153125 4 0.4040 0.69351 0.000 0.248 0.000 0.752
#> GSM153126 4 0.5836 0.67971 0.000 0.188 0.112 0.700
#> GSM153127 2 0.1890 0.80604 0.000 0.936 0.008 0.056
#> GSM153128 2 0.2840 0.81565 0.000 0.900 0.056 0.044
#> GSM153129 2 0.3168 0.80752 0.000 0.884 0.056 0.060
#> GSM153130 2 0.4638 0.78503 0.000 0.776 0.180 0.044
#> GSM153131 2 0.4072 0.79050 0.000 0.828 0.120 0.052
#> GSM153132 2 0.2255 0.81323 0.000 0.920 0.068 0.012
#> GSM153133 2 0.3052 0.77752 0.000 0.860 0.004 0.136
#> GSM153134 2 0.2542 0.80701 0.000 0.904 0.084 0.012
#> GSM153135 2 0.1661 0.80223 0.000 0.944 0.004 0.052
#> GSM153136 4 0.0188 0.81137 0.000 0.004 0.000 0.996
#> GSM153137 2 0.1792 0.79554 0.000 0.932 0.000 0.068
#> GSM153138 2 0.0707 0.80221 0.000 0.980 0.000 0.020
#> GSM153139 2 0.2530 0.80043 0.000 0.888 0.112 0.000
#> GSM153140 2 0.2814 0.77113 0.000 0.868 0.000 0.132
#> GSM153141 2 0.0817 0.80166 0.000 0.976 0.000 0.024
#> GSM153142 2 0.4877 0.70703 0.000 0.592 0.408 0.000
#> GSM153143 2 0.7114 0.59160 0.000 0.560 0.188 0.252
#> GSM153144 2 0.5489 0.59937 0.000 0.700 0.060 0.240
#> GSM153145 2 0.4907 0.70123 0.000 0.580 0.420 0.000
#> GSM153146 2 0.2060 0.81351 0.000 0.932 0.052 0.016
#> GSM153147 4 0.5292 0.70443 0.000 0.208 0.064 0.728
#> GSM153148 2 0.0817 0.80166 0.000 0.976 0.000 0.024
#> GSM153149 2 0.1182 0.80572 0.000 0.968 0.016 0.016
#> GSM153150 4 0.2704 0.78543 0.000 0.124 0.000 0.876
#> GSM153151 2 0.5132 0.75122 0.000 0.748 0.068 0.184
#> GSM153152 2 0.5484 0.68280 0.000 0.732 0.104 0.164
#> GSM153153 2 0.1042 0.80553 0.000 0.972 0.008 0.020
#> GSM153154 2 0.7113 0.56520 0.000 0.484 0.384 0.132
#> GSM153155 2 0.3390 0.77032 0.000 0.852 0.016 0.132
#> GSM153156 2 0.4956 0.77397 0.000 0.776 0.116 0.108
#> GSM153157 2 0.5365 0.75934 0.000 0.692 0.264 0.044
#> GSM153158 2 0.5112 0.71845 0.000 0.608 0.384 0.008
#> GSM153159 2 0.4916 0.69918 0.000 0.576 0.424 0.000
#> GSM153160 4 0.6544 0.56676 0.000 0.284 0.112 0.604
#> GSM153161 2 0.1118 0.80141 0.000 0.964 0.000 0.036
#> GSM153162 4 0.7181 0.47585 0.000 0.336 0.152 0.512
#> GSM153163 2 0.3908 0.79010 0.000 0.784 0.212 0.004
#> GSM153164 2 0.5130 0.72899 0.000 0.652 0.332 0.016
#> GSM153165 2 0.2530 0.80043 0.000 0.888 0.112 0.000
#> GSM153166 2 0.0937 0.80638 0.000 0.976 0.012 0.012
#> GSM153167 2 0.1174 0.80849 0.000 0.968 0.020 0.012
#> GSM153168 2 0.4877 0.70641 0.000 0.592 0.408 0.000
#> GSM153169 2 0.2714 0.80126 0.000 0.884 0.112 0.004
#> GSM153170 2 0.5272 0.75285 0.000 0.752 0.136 0.112
#> GSM153171 4 0.3688 0.73840 0.000 0.208 0.000 0.792
#> GSM153172 2 0.0592 0.80219 0.000 0.984 0.000 0.016
#> GSM153173 2 0.6893 0.65163 0.000 0.564 0.300 0.136
#> GSM153174 4 0.5478 0.68052 0.000 0.248 0.056 0.696
#> GSM153175 4 0.2918 0.79202 0.000 0.116 0.008 0.876
#> GSM153176 4 0.1059 0.80467 0.000 0.016 0.012 0.972
#> GSM153177 2 0.0927 0.80479 0.000 0.976 0.008 0.016
#> GSM152931 4 0.0188 0.81137 0.000 0.004 0.000 0.996
#> GSM152932 2 0.0707 0.80215 0.000 0.980 0.000 0.020
#> GSM152933 2 0.1854 0.81369 0.000 0.940 0.048 0.012
#> GSM152934 4 0.0707 0.81376 0.000 0.020 0.000 0.980
#> GSM152935 2 0.4485 0.78333 0.000 0.740 0.248 0.012
#> GSM152936 4 0.3355 0.77577 0.000 0.160 0.004 0.836
#> GSM152937 2 0.3301 0.80691 0.000 0.876 0.048 0.076
#> GSM152938 2 0.6597 0.36220 0.000 0.588 0.108 0.304
#> GSM152939 4 0.0336 0.81000 0.000 0.008 0.000 0.992
#> GSM152940 4 0.0188 0.81137 0.000 0.004 0.000 0.996
#> GSM152941 1 0.5329 0.31269 0.568 0.012 0.000 0.420
#> GSM152942 4 0.4036 0.76133 0.000 0.076 0.088 0.836
#> GSM152943 2 0.4761 0.48425 0.000 0.628 0.000 0.372
#> GSM152944 2 0.4830 0.71418 0.000 0.608 0.392 0.000
#> GSM152945 2 0.5161 0.73607 0.000 0.676 0.300 0.024
#> GSM152946 2 0.3219 0.74959 0.000 0.836 0.000 0.164
#> GSM152947 4 0.0469 0.81301 0.000 0.012 0.000 0.988
#> GSM152948 2 0.0707 0.80215 0.000 0.980 0.000 0.020
#> GSM152949 4 0.7553 0.28814 0.000 0.308 0.216 0.476
#> GSM152950 2 0.7681 -0.05803 0.000 0.404 0.216 0.380
#> GSM152951 2 0.4372 0.61821 0.000 0.728 0.004 0.268
#> GSM152952 2 0.1302 0.80175 0.000 0.956 0.000 0.044
#> GSM152953 2 0.0707 0.80215 0.000 0.980 0.000 0.020
#> GSM152954 4 0.2859 0.76913 0.000 0.112 0.008 0.880
#> GSM152955 2 0.5690 0.74108 0.000 0.672 0.268 0.060
#> GSM152956 2 0.0817 0.80166 0.000 0.976 0.000 0.024
#> GSM152957 4 0.0921 0.81277 0.000 0.028 0.000 0.972
#> GSM152958 4 0.0188 0.81137 0.000 0.004 0.000 0.996
#> GSM152959 4 0.0188 0.81137 0.000 0.004 0.000 0.996
#> GSM152960 2 0.5000 0.11596 0.000 0.504 0.000 0.496
#> GSM152961 4 0.0188 0.81137 0.000 0.004 0.000 0.996
#> GSM152962 2 0.2256 0.81292 0.000 0.924 0.056 0.020
#> GSM152963 2 0.1940 0.79799 0.000 0.924 0.000 0.076
#> GSM152964 2 0.6508 0.67283 0.000 0.556 0.360 0.084
#> GSM152965 2 0.0817 0.80327 0.000 0.976 0.000 0.024
#> GSM152966 4 0.0188 0.81137 0.000 0.004 0.000 0.996
#> GSM152967 4 0.4697 0.60819 0.000 0.356 0.000 0.644
#> GSM152968 2 0.3828 0.79535 0.000 0.848 0.084 0.068
#> GSM152969 4 0.5161 -0.18168 0.000 0.476 0.004 0.520
#> GSM152970 4 0.2589 0.79426 0.000 0.116 0.000 0.884
#> GSM152971 4 0.0188 0.81137 0.000 0.004 0.000 0.996
#> GSM152972 4 0.0188 0.81137 0.000 0.004 0.000 0.996
#> GSM152973 4 0.3182 0.77436 0.000 0.028 0.096 0.876
#> GSM152974 2 0.2124 0.81086 0.000 0.932 0.040 0.028
#> GSM152975 4 0.4767 0.67744 0.000 0.256 0.020 0.724
#> GSM152976 4 0.3813 0.77585 0.000 0.148 0.024 0.828
#> GSM152977 4 0.1635 0.80695 0.000 0.044 0.008 0.948
#> GSM152978 4 0.4973 0.34562 0.000 0.348 0.008 0.644
#> GSM152979 2 0.4304 0.76912 0.000 0.716 0.284 0.000
#> GSM152980 2 0.3088 0.78572 0.000 0.864 0.008 0.128
#> GSM152981 2 0.4916 0.69918 0.000 0.576 0.424 0.000
#> GSM152982 4 0.1890 0.80838 0.000 0.056 0.008 0.936
#> GSM152983 4 0.0188 0.81137 0.000 0.004 0.000 0.996
#> GSM152984 4 0.5716 0.68548 0.000 0.252 0.068 0.680
#> GSM152985 4 0.0376 0.80871 0.004 0.004 0.000 0.992
#> GSM152986 4 0.0469 0.81269 0.000 0.012 0.000 0.988
#> GSM152987 1 0.5689 0.40421 0.656 0.040 0.004 0.300
#> GSM152988 4 0.0927 0.81190 0.000 0.008 0.016 0.976
#> GSM152989 4 0.0188 0.81137 0.000 0.004 0.000 0.996
#> GSM152990 2 0.4477 0.77650 0.000 0.808 0.108 0.084
#> GSM152991 2 0.4252 0.76812 0.000 0.744 0.252 0.004
#> GSM187524 1 0.2847 0.74235 0.896 0.004 0.016 0.084
#> GSM187525 1 0.1867 0.78157 0.928 0.000 0.000 0.072
#> GSM187526 1 0.3208 0.68535 0.848 0.004 0.000 0.148
#> GSM187527 3 0.7178 0.60784 0.204 0.004 0.576 0.216
#> GSM152856 3 0.5080 0.89871 0.420 0.000 0.576 0.004
#> GSM152857 3 0.7103 0.67863 0.240 0.008 0.592 0.160
#> GSM152858 1 0.0336 0.81741 0.992 0.000 0.008 0.000
#> GSM152859 1 0.0188 0.82793 0.996 0.000 0.000 0.004
#> GSM152860 1 0.0188 0.82793 0.996 0.000 0.000 0.004
#> GSM152861 1 0.0188 0.82750 0.996 0.000 0.000 0.004
#> GSM152862 1 0.0188 0.82793 0.996 0.000 0.000 0.004
#> GSM152863 1 0.0188 0.82735 0.996 0.000 0.000 0.004
#> GSM152864 1 0.0000 0.82533 1.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.82533 1.000 0.000 0.000 0.000
#> GSM152866 3 0.5498 0.88833 0.404 0.000 0.576 0.020
#> GSM152867 1 0.0000 0.82533 1.000 0.000 0.000 0.000
#> GSM152868 1 0.2530 0.73665 0.888 0.000 0.000 0.112
#> GSM152869 1 0.2921 0.70037 0.860 0.000 0.000 0.140
#> GSM152870 1 0.0469 0.82432 0.988 0.000 0.000 0.012
#> GSM152871 1 0.0000 0.82533 1.000 0.000 0.000 0.000
#> GSM152872 1 0.0000 0.82533 1.000 0.000 0.000 0.000
#> GSM152873 3 0.5080 0.89871 0.420 0.000 0.576 0.004
#> GSM152874 3 0.5080 0.89871 0.420 0.000 0.576 0.004
#> GSM152875 3 0.5080 0.89871 0.420 0.000 0.576 0.004
#> GSM152876 3 0.5660 0.88188 0.396 0.000 0.576 0.028
#> GSM152877 3 0.5080 0.89871 0.420 0.000 0.576 0.004
#> GSM152878 3 0.6156 0.85514 0.372 0.004 0.576 0.048
#> GSM152879 3 0.5080 0.89871 0.420 0.000 0.576 0.004
#> GSM152880 3 0.5080 0.89871 0.420 0.000 0.576 0.004
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.1544 0.7140 0.000 0.932 0.000 0.068 0.000
#> GSM152805 5 0.4429 0.7351 0.000 0.192 0.064 0.000 0.744
#> GSM152806 5 0.3039 0.7654 0.000 0.192 0.000 0.000 0.808
#> GSM152807 2 0.2388 0.6895 0.000 0.900 0.000 0.072 0.028
#> GSM152808 5 0.2966 0.7642 0.000 0.184 0.000 0.000 0.816
#> GSM152809 2 0.4533 0.0418 0.000 0.544 0.000 0.448 0.008
#> GSM152810 4 0.6409 0.3363 0.000 0.404 0.052 0.488 0.056
#> GSM152811 2 0.7458 0.0989 0.000 0.468 0.172 0.068 0.292
#> GSM152812 2 0.0162 0.7325 0.000 0.996 0.000 0.000 0.004
#> GSM152813 2 0.1026 0.7378 0.000 0.968 0.004 0.024 0.004
#> GSM152814 2 0.0794 0.7274 0.000 0.972 0.000 0.000 0.028
#> GSM152815 2 0.0000 0.7323 0.000 1.000 0.000 0.000 0.000
#> GSM152816 2 0.2863 0.7039 0.000 0.876 0.060 0.000 0.064
#> GSM152817 5 0.3003 0.7650 0.000 0.188 0.000 0.000 0.812
#> GSM152818 5 0.2966 0.7642 0.000 0.184 0.000 0.000 0.816
#> GSM152819 2 0.4126 -0.0575 0.000 0.620 0.000 0.000 0.380
#> GSM152820 2 0.3537 0.7046 0.000 0.856 0.040 0.052 0.052
#> GSM152821 2 0.0162 0.7332 0.000 0.996 0.000 0.000 0.004
#> GSM153115 4 0.2966 0.7177 0.000 0.184 0.000 0.816 0.000
#> GSM153116 5 0.4235 0.6862 0.000 0.424 0.000 0.000 0.576
#> GSM153117 5 0.4256 0.6672 0.000 0.436 0.000 0.000 0.564
#> GSM153118 2 0.2732 0.6164 0.000 0.840 0.000 0.000 0.160
#> GSM153119 5 0.4150 0.7023 0.000 0.388 0.000 0.000 0.612
#> GSM153120 4 0.0000 0.7669 0.000 0.000 0.000 1.000 0.000
#> GSM153121 5 0.6860 0.4127 0.000 0.396 0.176 0.016 0.412
#> GSM153122 2 0.6624 0.4674 0.000 0.608 0.200 0.068 0.124
#> GSM153123 2 0.2069 0.7306 0.000 0.912 0.076 0.000 0.012
#> GSM153124 2 0.3160 0.6258 0.000 0.808 0.000 0.188 0.004
#> GSM153125 4 0.3508 0.6661 0.000 0.252 0.000 0.748 0.000
#> GSM153126 4 0.6810 0.5488 0.000 0.144 0.200 0.588 0.068
#> GSM153127 2 0.1364 0.7329 0.000 0.952 0.000 0.036 0.012
#> GSM153128 2 0.2927 0.7222 0.000 0.888 0.028 0.036 0.048
#> GSM153129 2 0.4397 0.6787 0.000 0.800 0.100 0.044 0.056
#> GSM153130 2 0.5712 0.5587 0.000 0.672 0.200 0.028 0.100
#> GSM153131 2 0.5737 0.5675 0.000 0.676 0.200 0.040 0.084
#> GSM153132 2 0.2728 0.7128 0.000 0.888 0.040 0.004 0.068
#> GSM153133 2 0.2843 0.6774 0.000 0.848 0.000 0.144 0.008
#> GSM153134 2 0.3452 0.6871 0.000 0.820 0.148 0.000 0.032
#> GSM153135 2 0.0865 0.7358 0.000 0.972 0.000 0.024 0.004
#> GSM153136 4 0.0162 0.7681 0.000 0.004 0.000 0.996 0.000
#> GSM153137 2 0.0963 0.7281 0.000 0.964 0.000 0.036 0.000
#> GSM153138 2 0.0000 0.7323 0.000 1.000 0.000 0.000 0.000
#> GSM153139 2 0.4429 0.6303 0.000 0.744 0.192 0.000 0.064
#> GSM153140 2 0.2329 0.6864 0.000 0.876 0.000 0.124 0.000
#> GSM153141 2 0.0000 0.7323 0.000 1.000 0.000 0.000 0.000
#> GSM153142 5 0.3274 0.7697 0.000 0.220 0.000 0.000 0.780
#> GSM153143 2 0.6475 -0.4542 0.000 0.428 0.000 0.184 0.388
#> GSM153144 2 0.5344 0.5159 0.000 0.692 0.104 0.192 0.012
#> GSM153145 5 0.2966 0.7642 0.000 0.184 0.000 0.000 0.816
#> GSM153146 2 0.2104 0.7190 0.000 0.916 0.024 0.000 0.060
#> GSM153147 4 0.5795 0.6326 0.000 0.192 0.120 0.664 0.024
#> GSM153148 2 0.0000 0.7323 0.000 1.000 0.000 0.000 0.000
#> GSM153149 2 0.1502 0.7378 0.000 0.940 0.056 0.000 0.004
#> GSM153150 4 0.2377 0.7461 0.000 0.128 0.000 0.872 0.000
#> GSM153151 2 0.5437 0.5948 0.000 0.704 0.112 0.160 0.024
#> GSM153152 2 0.6397 0.4430 0.000 0.648 0.092 0.144 0.116
#> GSM153153 2 0.0404 0.7337 0.000 0.988 0.000 0.000 0.012
#> GSM153154 5 0.5641 0.7026 0.000 0.312 0.004 0.088 0.596
#> GSM153155 2 0.2886 0.6875 0.000 0.864 0.016 0.116 0.004
#> GSM153156 2 0.5519 0.5924 0.000 0.692 0.200 0.040 0.068
#> GSM153157 2 0.6076 0.4794 0.000 0.652 0.124 0.040 0.184
#> GSM153158 5 0.4235 0.6789 0.000 0.424 0.000 0.000 0.576
#> GSM153159 5 0.4138 0.7037 0.000 0.384 0.000 0.000 0.616
#> GSM153160 4 0.7269 0.4613 0.000 0.208 0.200 0.524 0.068
#> GSM153161 2 0.0404 0.7330 0.000 0.988 0.000 0.012 0.000
#> GSM153162 4 0.7501 0.4649 0.000 0.284 0.128 0.484 0.104
#> GSM153163 2 0.4982 0.5884 0.000 0.700 0.200 0.000 0.100
#> GSM153164 5 0.4397 0.6715 0.000 0.432 0.000 0.004 0.564
#> GSM153165 2 0.4555 0.6191 0.000 0.732 0.200 0.000 0.068
#> GSM153166 2 0.0912 0.7369 0.000 0.972 0.016 0.000 0.012
#> GSM153167 2 0.1300 0.7399 0.000 0.956 0.028 0.000 0.016
#> GSM153168 5 0.3003 0.7649 0.000 0.188 0.000 0.000 0.812
#> GSM153169 2 0.4522 0.6242 0.000 0.736 0.196 0.000 0.068
#> GSM153170 2 0.6437 0.5118 0.000 0.628 0.200 0.088 0.084
#> GSM153171 4 0.3395 0.6904 0.000 0.236 0.000 0.764 0.000
#> GSM153172 2 0.0324 0.7340 0.000 0.992 0.004 0.000 0.004
#> GSM153173 2 0.7762 0.1361 0.000 0.476 0.200 0.112 0.212
#> GSM153174 4 0.5972 0.6218 0.000 0.224 0.108 0.640 0.028
#> GSM153175 4 0.2462 0.7557 0.000 0.112 0.008 0.880 0.000
#> GSM153176 4 0.0771 0.7659 0.000 0.000 0.004 0.976 0.020
#> GSM153177 2 0.1281 0.7387 0.000 0.956 0.032 0.000 0.012
#> GSM152931 4 0.0162 0.7681 0.000 0.004 0.000 0.996 0.000
#> GSM152932 2 0.0324 0.7340 0.000 0.992 0.004 0.000 0.004
#> GSM152933 2 0.1907 0.7310 0.000 0.928 0.044 0.000 0.028
#> GSM152934 4 0.0404 0.7694 0.000 0.012 0.000 0.988 0.000
#> GSM152935 2 0.4891 0.5514 0.000 0.716 0.112 0.000 0.172
#> GSM152936 4 0.3266 0.7193 0.000 0.200 0.004 0.796 0.000
#> GSM152937 2 0.3595 0.7136 0.000 0.852 0.064 0.044 0.040
#> GSM152938 2 0.7566 0.2093 0.000 0.444 0.200 0.292 0.064
#> GSM152939 4 0.0162 0.7681 0.000 0.004 0.000 0.996 0.000
#> GSM152940 4 0.0000 0.7669 0.000 0.000 0.000 1.000 0.000
#> GSM152941 1 0.4549 0.2478 0.528 0.008 0.000 0.464 0.000
#> GSM152942 4 0.4937 0.6883 0.000 0.056 0.128 0.760 0.056
#> GSM152943 2 0.4126 0.3410 0.000 0.620 0.000 0.380 0.000
#> GSM152944 2 0.6363 -0.3159 0.000 0.444 0.164 0.000 0.392
#> GSM152945 5 0.4437 0.6127 0.000 0.464 0.000 0.004 0.532
#> GSM152946 2 0.2964 0.6640 0.000 0.840 0.004 0.152 0.004
#> GSM152947 4 0.0404 0.7699 0.000 0.012 0.000 0.988 0.000
#> GSM152948 2 0.0000 0.7323 0.000 1.000 0.000 0.000 0.000
#> GSM152949 4 0.8312 0.1190 0.000 0.228 0.200 0.388 0.184
#> GSM152950 4 0.7780 -0.1159 0.000 0.304 0.056 0.332 0.308
#> GSM152951 2 0.3508 0.5168 0.000 0.748 0.000 0.252 0.000
#> GSM152952 2 0.0510 0.7331 0.000 0.984 0.000 0.016 0.000
#> GSM152953 2 0.0000 0.7323 0.000 1.000 0.000 0.000 0.000
#> GSM152954 4 0.2304 0.7347 0.000 0.100 0.000 0.892 0.008
#> GSM152955 2 0.4987 0.0600 0.000 0.616 0.000 0.044 0.340
#> GSM152956 2 0.0000 0.7323 0.000 1.000 0.000 0.000 0.000
#> GSM152957 4 0.1121 0.7696 0.000 0.044 0.000 0.956 0.000
#> GSM152958 4 0.0000 0.7669 0.000 0.000 0.000 1.000 0.000
#> GSM152959 4 0.0000 0.7669 0.000 0.000 0.000 1.000 0.000
#> GSM152960 4 0.4302 -0.0308 0.000 0.480 0.000 0.520 0.000
#> GSM152961 4 0.0000 0.7669 0.000 0.000 0.000 1.000 0.000
#> GSM152962 2 0.2067 0.7344 0.000 0.920 0.048 0.000 0.032
#> GSM152963 2 0.1043 0.7311 0.000 0.960 0.000 0.040 0.000
#> GSM152964 2 0.6486 -0.5037 0.000 0.444 0.056 0.056 0.444
#> GSM152965 2 0.0404 0.7359 0.000 0.988 0.012 0.000 0.000
#> GSM152966 4 0.0000 0.7669 0.000 0.000 0.000 1.000 0.000
#> GSM152967 4 0.4161 0.5480 0.000 0.392 0.000 0.608 0.000
#> GSM152968 2 0.5105 0.6349 0.000 0.744 0.144 0.052 0.060
#> GSM152969 4 0.4437 -0.0902 0.000 0.464 0.000 0.532 0.004
#> GSM152970 4 0.2389 0.7544 0.000 0.116 0.000 0.880 0.004
#> GSM152971 4 0.0000 0.7669 0.000 0.000 0.000 1.000 0.000
#> GSM152972 4 0.0000 0.7669 0.000 0.000 0.000 1.000 0.000
#> GSM152973 4 0.4449 0.6912 0.000 0.020 0.140 0.780 0.060
#> GSM152974 2 0.1967 0.7378 0.000 0.932 0.036 0.012 0.020
#> GSM152975 4 0.4054 0.6691 0.000 0.248 0.000 0.732 0.020
#> GSM152976 4 0.4109 0.7223 0.000 0.168 0.048 0.780 0.004
#> GSM152977 4 0.0992 0.7670 0.000 0.024 0.000 0.968 0.008
#> GSM152978 4 0.4218 0.3826 0.000 0.332 0.000 0.660 0.008
#> GSM152979 2 0.5452 0.5247 0.000 0.656 0.200 0.000 0.144
#> GSM152980 2 0.2833 0.7014 0.000 0.864 0.004 0.120 0.012
#> GSM152981 5 0.4045 0.7358 0.000 0.356 0.000 0.000 0.644
#> GSM152982 4 0.1830 0.7673 0.000 0.052 0.012 0.932 0.004
#> GSM152983 4 0.0000 0.7669 0.000 0.000 0.000 1.000 0.000
#> GSM152984 4 0.6150 0.6162 0.000 0.248 0.104 0.616 0.032
#> GSM152985 4 0.0000 0.7669 0.000 0.000 0.000 1.000 0.000
#> GSM152986 4 0.0404 0.7697 0.000 0.012 0.000 0.988 0.000
#> GSM152987 1 0.5483 0.4620 0.616 0.052 0.016 0.316 0.000
#> GSM152988 4 0.1012 0.7691 0.000 0.012 0.020 0.968 0.000
#> GSM152989 4 0.0000 0.7669 0.000 0.000 0.000 1.000 0.000
#> GSM152990 2 0.5870 0.5630 0.000 0.672 0.196 0.060 0.072
#> GSM152991 2 0.4225 0.0367 0.000 0.632 0.004 0.000 0.364
#> GSM187524 1 0.4768 0.7128 0.780 0.004 0.044 0.112 0.060
#> GSM187525 1 0.2378 0.7824 0.908 0.000 0.016 0.064 0.012
#> GSM187526 1 0.2424 0.7319 0.868 0.000 0.000 0.132 0.000
#> GSM187527 3 0.3846 0.8975 0.144 0.000 0.800 0.056 0.000
#> GSM152856 3 0.3109 0.9837 0.200 0.000 0.800 0.000 0.000
#> GSM152857 3 0.3849 0.9411 0.164 0.000 0.800 0.020 0.016
#> GSM152858 1 0.3456 0.7715 0.800 0.000 0.016 0.000 0.184
#> GSM152859 1 0.3456 0.7723 0.800 0.000 0.016 0.000 0.184
#> GSM152860 1 0.3550 0.7694 0.796 0.000 0.020 0.000 0.184
#> GSM152861 1 0.0162 0.7916 0.996 0.000 0.000 0.004 0.000
#> GSM152862 1 0.3639 0.7669 0.792 0.000 0.024 0.000 0.184
#> GSM152863 1 0.0162 0.7888 0.996 0.000 0.004 0.000 0.000
#> GSM152864 1 0.0000 0.7902 1.000 0.000 0.000 0.000 0.000
#> GSM152865 1 0.0162 0.7909 0.996 0.000 0.000 0.004 0.000
#> GSM152866 3 0.3300 0.9746 0.204 0.000 0.792 0.004 0.000
#> GSM152867 1 0.0000 0.7902 1.000 0.000 0.000 0.000 0.000
#> GSM152868 1 0.1908 0.7642 0.908 0.000 0.000 0.092 0.000
#> GSM152869 1 0.2280 0.7411 0.880 0.000 0.000 0.120 0.000
#> GSM152870 1 0.3525 0.7778 0.800 0.000 0.008 0.008 0.184
#> GSM152871 1 0.2966 0.7767 0.816 0.000 0.000 0.000 0.184
#> GSM152872 1 0.3123 0.7761 0.812 0.000 0.004 0.000 0.184
#> GSM152873 3 0.3109 0.9837 0.200 0.000 0.800 0.000 0.000
#> GSM152874 3 0.3109 0.9837 0.200 0.000 0.800 0.000 0.000
#> GSM152875 3 0.3109 0.9837 0.200 0.000 0.800 0.000 0.000
#> GSM152876 3 0.3109 0.9837 0.200 0.000 0.800 0.000 0.000
#> GSM152877 3 0.3109 0.9837 0.200 0.000 0.800 0.000 0.000
#> GSM152878 3 0.3109 0.9837 0.200 0.000 0.800 0.000 0.000
#> GSM152879 3 0.3109 0.9837 0.200 0.000 0.800 0.000 0.000
#> GSM152880 3 0.3109 0.9837 0.200 0.000 0.800 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.1225 0.7137 0.000 0.952 0.012 0.036 0.000 0.000
#> GSM152805 5 0.3076 0.3043 0.000 0.000 0.240 0.000 0.760 0.000
#> GSM152806 5 0.0146 0.4943 0.000 0.004 0.000 0.000 0.996 0.000
#> GSM152807 2 0.1952 0.6896 0.000 0.920 0.012 0.052 0.016 0.000
#> GSM152808 5 0.0000 0.4933 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152809 2 0.4084 0.1578 0.000 0.588 0.012 0.400 0.000 0.000
#> GSM152810 4 0.5967 0.2369 0.000 0.428 0.096 0.440 0.036 0.000
#> GSM152811 3 0.6023 -0.0847 0.000 0.180 0.408 0.008 0.404 0.000
#> GSM152812 2 0.0363 0.7154 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152813 2 0.1749 0.7167 0.000 0.932 0.024 0.036 0.008 0.000
#> GSM152814 2 0.0909 0.7119 0.000 0.968 0.012 0.000 0.020 0.000
#> GSM152815 2 0.0363 0.7154 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152816 2 0.3641 0.6162 0.000 0.732 0.248 0.000 0.020 0.000
#> GSM152817 5 0.0146 0.4939 0.000 0.004 0.000 0.000 0.996 0.000
#> GSM152818 5 0.0000 0.4933 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152819 2 0.3993 0.1230 0.000 0.592 0.008 0.000 0.400 0.000
#> GSM152820 2 0.4121 0.6478 0.000 0.756 0.180 0.040 0.024 0.000
#> GSM152821 2 0.0603 0.7188 0.000 0.980 0.004 0.000 0.016 0.000
#> GSM153115 4 0.3431 0.6403 0.000 0.228 0.016 0.756 0.000 0.000
#> GSM153116 5 0.3737 0.5179 0.000 0.392 0.000 0.000 0.608 0.000
#> GSM153117 5 0.3756 0.5072 0.000 0.400 0.000 0.000 0.600 0.000
#> GSM153118 2 0.2814 0.6168 0.000 0.820 0.008 0.000 0.172 0.000
#> GSM153119 5 0.3955 0.5152 0.000 0.384 0.008 0.000 0.608 0.000
#> GSM153120 4 0.0000 0.7450 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153121 2 0.6425 0.0731 0.000 0.380 0.344 0.016 0.260 0.000
#> GSM153122 2 0.4719 0.4780 0.000 0.516 0.448 0.016 0.020 0.000
#> GSM153123 2 0.2278 0.7133 0.000 0.868 0.128 0.000 0.004 0.000
#> GSM153124 2 0.3253 0.6192 0.000 0.788 0.020 0.192 0.000 0.000
#> GSM153125 4 0.3534 0.6179 0.000 0.244 0.016 0.740 0.000 0.000
#> GSM153126 4 0.5317 0.2500 0.000 0.056 0.448 0.476 0.020 0.000
#> GSM153127 2 0.1750 0.7167 0.000 0.932 0.012 0.040 0.016 0.000
#> GSM153128 2 0.3411 0.6992 0.000 0.836 0.088 0.044 0.032 0.000
#> GSM153129 2 0.4305 0.5789 0.000 0.656 0.312 0.012 0.020 0.000
#> GSM153130 2 0.4314 0.4954 0.000 0.536 0.444 0.000 0.020 0.000
#> GSM153131 2 0.4442 0.4948 0.000 0.536 0.440 0.004 0.020 0.000
#> GSM153132 2 0.3640 0.6432 0.000 0.764 0.204 0.004 0.028 0.000
#> GSM153133 2 0.2920 0.6555 0.000 0.820 0.008 0.168 0.004 0.000
#> GSM153134 2 0.3298 0.6621 0.000 0.756 0.236 0.000 0.008 0.000
#> GSM153135 2 0.0993 0.7163 0.000 0.964 0.012 0.024 0.000 0.000
#> GSM153136 4 0.0405 0.7460 0.000 0.004 0.008 0.988 0.000 0.000
#> GSM153137 2 0.0993 0.7131 0.000 0.964 0.012 0.024 0.000 0.000
#> GSM153138 2 0.0000 0.7173 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM153139 2 0.4218 0.5144 0.000 0.556 0.428 0.000 0.016 0.000
#> GSM153140 2 0.2320 0.6717 0.000 0.864 0.004 0.132 0.000 0.000
#> GSM153141 2 0.0363 0.7154 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM153142 5 0.1327 0.5414 0.000 0.064 0.000 0.000 0.936 0.000
#> GSM153143 2 0.5819 -0.2497 0.000 0.420 0.000 0.184 0.396 0.000
#> GSM153144 2 0.4704 0.5455 0.000 0.684 0.160 0.156 0.000 0.000
#> GSM153145 5 0.0000 0.4933 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153146 2 0.2889 0.6722 0.000 0.848 0.044 0.000 0.108 0.000
#> GSM153147 4 0.5170 0.5244 0.000 0.204 0.176 0.620 0.000 0.000
#> GSM153148 2 0.0260 0.7162 0.000 0.992 0.008 0.000 0.000 0.000
#> GSM153149 2 0.1556 0.7236 0.000 0.920 0.080 0.000 0.000 0.000
#> GSM153150 4 0.2389 0.7120 0.000 0.128 0.008 0.864 0.000 0.000
#> GSM153151 2 0.5570 0.5101 0.000 0.600 0.152 0.232 0.016 0.000
#> GSM153152 2 0.6172 0.4450 0.000 0.604 0.140 0.132 0.124 0.000
#> GSM153153 2 0.0806 0.7187 0.000 0.972 0.008 0.000 0.020 0.000
#> GSM153154 5 0.5269 0.5373 0.000 0.292 0.016 0.088 0.604 0.000
#> GSM153155 2 0.2487 0.7016 0.000 0.876 0.032 0.092 0.000 0.000
#> GSM153156 2 0.4370 0.4965 0.000 0.536 0.444 0.004 0.016 0.000
#> GSM153157 2 0.5190 0.5077 0.000 0.576 0.324 0.004 0.096 0.000
#> GSM153158 5 0.3756 0.5072 0.000 0.400 0.000 0.000 0.600 0.000
#> GSM153159 5 0.3841 0.5199 0.000 0.380 0.004 0.000 0.616 0.000
#> GSM153160 3 0.5753 -0.2465 0.000 0.100 0.448 0.432 0.020 0.000
#> GSM153161 2 0.0820 0.7139 0.000 0.972 0.012 0.016 0.000 0.000
#> GSM153162 4 0.6522 0.3696 0.000 0.300 0.212 0.452 0.036 0.000
#> GSM153163 2 0.4385 0.4910 0.000 0.532 0.444 0.000 0.024 0.000
#> GSM153164 5 0.3737 0.5148 0.000 0.392 0.000 0.000 0.608 0.000
#> GSM153165 2 0.4314 0.4954 0.000 0.536 0.444 0.000 0.020 0.000
#> GSM153166 2 0.1349 0.7226 0.000 0.940 0.056 0.000 0.004 0.000
#> GSM153167 2 0.1866 0.7230 0.000 0.908 0.084 0.000 0.008 0.000
#> GSM153168 5 0.0000 0.4933 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153169 2 0.4294 0.5085 0.000 0.552 0.428 0.000 0.020 0.000
#> GSM153170 2 0.4984 0.4716 0.000 0.512 0.436 0.032 0.020 0.000
#> GSM153171 4 0.3729 0.5861 0.000 0.296 0.012 0.692 0.000 0.000
#> GSM153172 2 0.0363 0.7191 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM153173 3 0.5951 -0.4907 0.000 0.432 0.444 0.072 0.052 0.000
#> GSM153174 4 0.5639 0.4738 0.000 0.184 0.236 0.572 0.008 0.000
#> GSM153175 4 0.2383 0.7253 0.000 0.096 0.024 0.880 0.000 0.000
#> GSM153176 4 0.1088 0.7398 0.000 0.000 0.024 0.960 0.016 0.000
#> GSM153177 2 0.1644 0.7235 0.000 0.920 0.076 0.000 0.004 0.000
#> GSM152931 4 0.0291 0.7465 0.000 0.004 0.004 0.992 0.000 0.000
#> GSM152932 2 0.0363 0.7191 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152933 2 0.2706 0.6976 0.000 0.852 0.124 0.000 0.024 0.000
#> GSM152934 4 0.0520 0.7466 0.000 0.008 0.008 0.984 0.000 0.000
#> GSM152935 2 0.4638 0.5805 0.000 0.692 0.152 0.000 0.156 0.000
#> GSM152936 4 0.3778 0.6099 0.000 0.272 0.020 0.708 0.000 0.000
#> GSM152937 2 0.2921 0.6980 0.000 0.828 0.156 0.008 0.008 0.000
#> GSM152938 3 0.6343 -0.1720 0.000 0.296 0.452 0.232 0.020 0.000
#> GSM152939 4 0.0508 0.7463 0.000 0.004 0.012 0.984 0.000 0.000
#> GSM152940 4 0.0000 0.7450 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152941 4 0.4460 0.0199 0.000 0.000 0.452 0.520 0.000 0.028
#> GSM152942 4 0.4653 0.4901 0.000 0.032 0.304 0.644 0.020 0.000
#> GSM152943 2 0.4101 0.3673 0.000 0.580 0.012 0.408 0.000 0.000
#> GSM152944 2 0.6007 0.1786 0.000 0.424 0.324 0.000 0.252 0.000
#> GSM152945 5 0.3930 0.4656 0.000 0.420 0.000 0.004 0.576 0.000
#> GSM152946 2 0.2859 0.6547 0.000 0.828 0.016 0.156 0.000 0.000
#> GSM152947 4 0.0508 0.7479 0.000 0.012 0.004 0.984 0.000 0.000
#> GSM152948 2 0.0363 0.7154 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152949 3 0.6571 -0.0846 0.000 0.188 0.444 0.324 0.044 0.000
#> GSM152950 4 0.7538 -0.0282 0.000 0.284 0.148 0.320 0.248 0.000
#> GSM152951 2 0.3287 0.5717 0.000 0.768 0.012 0.220 0.000 0.000
#> GSM152952 2 0.0363 0.7154 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152953 2 0.0146 0.7168 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM152954 4 0.1970 0.7030 0.000 0.092 0.000 0.900 0.008 0.000
#> GSM152955 2 0.4284 0.1719 0.000 0.596 0.008 0.012 0.384 0.000
#> GSM152956 2 0.0363 0.7154 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152957 4 0.1265 0.7450 0.000 0.044 0.008 0.948 0.000 0.000
#> GSM152958 4 0.0146 0.7452 0.000 0.000 0.004 0.996 0.000 0.000
#> GSM152959 4 0.0146 0.7448 0.000 0.000 0.004 0.996 0.000 0.000
#> GSM152960 4 0.4032 0.1330 0.000 0.420 0.008 0.572 0.000 0.000
#> GSM152961 4 0.0000 0.7450 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152962 2 0.2122 0.7197 0.000 0.900 0.076 0.000 0.024 0.000
#> GSM152963 2 0.0891 0.7219 0.000 0.968 0.008 0.024 0.000 0.000
#> GSM152964 5 0.5821 0.2320 0.000 0.428 0.080 0.036 0.456 0.000
#> GSM152965 2 0.0713 0.7206 0.000 0.972 0.028 0.000 0.000 0.000
#> GSM152966 4 0.0000 0.7450 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152967 4 0.4328 0.3995 0.000 0.460 0.020 0.520 0.000 0.000
#> GSM152968 2 0.4405 0.5443 0.000 0.604 0.368 0.008 0.020 0.000
#> GSM152969 4 0.4184 -0.0245 0.000 0.432 0.008 0.556 0.004 0.000
#> GSM152970 4 0.2110 0.7317 0.000 0.084 0.012 0.900 0.000 0.004
#> GSM152971 4 0.0000 0.7450 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152972 4 0.0000 0.7450 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152973 4 0.4379 0.5266 0.000 0.024 0.292 0.668 0.016 0.000
#> GSM152974 2 0.1820 0.7199 0.000 0.924 0.056 0.012 0.008 0.000
#> GSM152975 4 0.3371 0.6557 0.000 0.200 0.004 0.780 0.016 0.000
#> GSM152976 4 0.4223 0.6359 0.000 0.204 0.076 0.720 0.000 0.000
#> GSM152977 4 0.0993 0.7426 0.000 0.024 0.000 0.964 0.012 0.000
#> GSM152978 4 0.3844 0.3948 0.000 0.312 0.004 0.676 0.008 0.000
#> GSM152979 2 0.4509 0.4899 0.000 0.532 0.436 0.000 0.032 0.000
#> GSM152980 2 0.3537 0.6572 0.000 0.796 0.024 0.164 0.016 0.000
#> GSM152981 5 0.3607 0.5587 0.000 0.348 0.000 0.000 0.652 0.000
#> GSM152982 4 0.1700 0.7381 0.000 0.048 0.024 0.928 0.000 0.000
#> GSM152983 4 0.0146 0.7450 0.000 0.000 0.004 0.996 0.000 0.000
#> GSM152984 4 0.5802 0.4679 0.000 0.292 0.148 0.544 0.016 0.000
#> GSM152985 4 0.0000 0.7450 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152986 4 0.0806 0.7476 0.000 0.020 0.008 0.972 0.000 0.000
#> GSM152987 3 0.7253 0.0380 0.044 0.052 0.428 0.332 0.000 0.144
#> GSM152988 4 0.1498 0.7444 0.000 0.032 0.028 0.940 0.000 0.000
#> GSM152989 4 0.0000 0.7450 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152990 2 0.4542 0.4919 0.000 0.532 0.440 0.008 0.020 0.000
#> GSM152991 2 0.4057 0.1363 0.000 0.600 0.012 0.000 0.388 0.000
#> GSM187524 3 0.7310 -0.1754 0.124 0.000 0.376 0.200 0.000 0.300
#> GSM187525 3 0.5658 0.0210 0.064 0.000 0.516 0.040 0.000 0.380
#> GSM187526 3 0.4741 0.0717 0.004 0.000 0.536 0.040 0.000 0.420
#> GSM187527 1 0.0146 0.9907 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM152856 1 0.0000 0.9967 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152857 1 0.0000 0.9967 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152858 6 0.0937 0.9546 0.040 0.000 0.000 0.000 0.000 0.960
#> GSM152859 6 0.1398 0.9484 0.052 0.000 0.008 0.000 0.000 0.940
#> GSM152860 6 0.1444 0.9394 0.072 0.000 0.000 0.000 0.000 0.928
#> GSM152861 3 0.3854 0.0329 0.000 0.000 0.536 0.000 0.000 0.464
#> GSM152862 6 0.1556 0.9314 0.080 0.000 0.000 0.000 0.000 0.920
#> GSM152863 3 0.4792 0.0636 0.044 0.000 0.536 0.004 0.000 0.416
#> GSM152864 3 0.4314 0.0618 0.020 0.000 0.536 0.000 0.000 0.444
#> GSM152865 3 0.4442 0.0708 0.020 0.000 0.536 0.004 0.000 0.440
#> GSM152866 1 0.0632 0.9701 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM152867 3 0.4370 0.0672 0.016 0.000 0.536 0.004 0.000 0.444
#> GSM152868 3 0.4466 0.0744 0.008 0.000 0.536 0.016 0.000 0.440
#> GSM152869 3 0.4442 0.0753 0.004 0.000 0.536 0.020 0.000 0.440
#> GSM152870 6 0.0935 0.9519 0.032 0.000 0.000 0.004 0.000 0.964
#> GSM152871 6 0.0146 0.9326 0.004 0.000 0.000 0.000 0.000 0.996
#> GSM152872 6 0.0458 0.9444 0.016 0.000 0.000 0.000 0.000 0.984
#> GSM152873 1 0.0000 0.9967 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.9967 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152875 1 0.0000 0.9967 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152876 1 0.0000 0.9967 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152877 1 0.0000 0.9967 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152878 1 0.0000 0.9967 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152879 1 0.0000 0.9967 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.9967 1.000 0.000 0.000 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> CV:pam 169 2.26e-28 2
#> CV:pam 163 1.23e-30 3
#> CV:pam 159 1.99e-30 4
#> CV:pam 146 1.87e-27 5
#> CV:pam 116 7.41e-24 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "mclust"]
# you can also extract it by
# res = res_list["CV:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.693 0.924 0.943 0.3318 0.701 0.701
#> 3 3 0.450 0.689 0.831 0.7032 0.667 0.530
#> 4 4 0.870 0.900 0.937 0.1964 0.923 0.803
#> 5 5 0.755 0.863 0.906 0.1349 0.858 0.586
#> 6 6 0.716 0.754 0.846 0.0342 0.973 0.882
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 4
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0938 0.940 0.012 0.988
#> GSM152805 2 0.4298 0.911 0.088 0.912
#> GSM152806 2 0.5059 0.895 0.112 0.888
#> GSM152807 2 0.2603 0.940 0.044 0.956
#> GSM152808 2 0.5059 0.895 0.112 0.888
#> GSM152809 2 0.2423 0.940 0.040 0.960
#> GSM152810 2 0.5059 0.895 0.112 0.888
#> GSM152811 2 0.4939 0.898 0.108 0.892
#> GSM152812 2 0.2423 0.940 0.040 0.960
#> GSM152813 2 0.0672 0.939 0.008 0.992
#> GSM152814 2 0.2423 0.940 0.040 0.960
#> GSM152815 2 0.2423 0.940 0.040 0.960
#> GSM152816 2 0.0000 0.937 0.000 1.000
#> GSM152817 2 0.5059 0.895 0.112 0.888
#> GSM152818 2 0.5059 0.895 0.112 0.888
#> GSM152819 2 0.0672 0.938 0.008 0.992
#> GSM152820 2 0.0376 0.938 0.004 0.996
#> GSM152821 2 0.2236 0.941 0.036 0.964
#> GSM153115 2 0.4690 0.918 0.100 0.900
#> GSM153116 2 0.4298 0.911 0.088 0.912
#> GSM153117 2 0.3431 0.924 0.064 0.936
#> GSM153118 2 0.0672 0.939 0.008 0.992
#> GSM153119 2 0.5059 0.895 0.112 0.888
#> GSM153120 2 0.6887 0.872 0.184 0.816
#> GSM153121 2 0.0000 0.937 0.000 1.000
#> GSM153122 2 0.5059 0.895 0.112 0.888
#> GSM153123 2 0.0000 0.937 0.000 1.000
#> GSM153124 2 0.4562 0.919 0.096 0.904
#> GSM153125 2 0.4431 0.921 0.092 0.908
#> GSM153126 2 0.0000 0.937 0.000 1.000
#> GSM153127 2 0.2423 0.940 0.040 0.960
#> GSM153128 2 0.2423 0.933 0.040 0.960
#> GSM153129 2 0.0000 0.937 0.000 1.000
#> GSM153130 2 0.0000 0.937 0.000 1.000
#> GSM153131 2 0.0376 0.938 0.004 0.996
#> GSM153132 2 0.0000 0.937 0.000 1.000
#> GSM153133 2 0.1414 0.940 0.020 0.980
#> GSM153134 2 0.0000 0.937 0.000 1.000
#> GSM153135 2 0.2423 0.940 0.040 0.960
#> GSM153136 2 0.6148 0.897 0.152 0.848
#> GSM153137 2 0.3114 0.937 0.056 0.944
#> GSM153138 2 0.2948 0.941 0.052 0.948
#> GSM153139 2 0.0000 0.937 0.000 1.000
#> GSM153140 2 0.2043 0.941 0.032 0.968
#> GSM153141 2 0.2603 0.940 0.044 0.956
#> GSM153142 2 0.4562 0.906 0.096 0.904
#> GSM153143 2 0.2423 0.940 0.040 0.960
#> GSM153144 2 0.0000 0.937 0.000 1.000
#> GSM153145 2 0.5059 0.895 0.112 0.888
#> GSM153146 2 0.2423 0.940 0.040 0.960
#> GSM153147 2 0.0000 0.937 0.000 1.000
#> GSM153148 2 0.2423 0.940 0.040 0.960
#> GSM153149 2 0.2423 0.940 0.040 0.960
#> GSM153150 2 0.6887 0.872 0.184 0.816
#> GSM153151 2 0.1414 0.940 0.020 0.980
#> GSM153152 2 0.0000 0.937 0.000 1.000
#> GSM153153 2 0.2423 0.940 0.040 0.960
#> GSM153154 2 0.0376 0.938 0.004 0.996
#> GSM153155 2 0.2236 0.940 0.036 0.964
#> GSM153156 2 0.0000 0.937 0.000 1.000
#> GSM153157 2 0.4298 0.911 0.088 0.912
#> GSM153158 2 0.3879 0.918 0.076 0.924
#> GSM153159 2 0.4562 0.906 0.096 0.904
#> GSM153160 2 0.0000 0.937 0.000 1.000
#> GSM153161 2 0.2603 0.940 0.044 0.956
#> GSM153162 2 0.0000 0.937 0.000 1.000
#> GSM153163 2 0.0000 0.937 0.000 1.000
#> GSM153164 2 0.3114 0.927 0.056 0.944
#> GSM153165 2 0.0000 0.937 0.000 1.000
#> GSM153166 2 0.0672 0.939 0.008 0.992
#> GSM153167 2 0.0000 0.937 0.000 1.000
#> GSM153168 2 0.5059 0.895 0.112 0.888
#> GSM153169 2 0.0000 0.937 0.000 1.000
#> GSM153170 2 0.0000 0.937 0.000 1.000
#> GSM153171 2 0.6148 0.897 0.152 0.848
#> GSM153172 2 0.2043 0.941 0.032 0.968
#> GSM153173 2 0.0000 0.937 0.000 1.000
#> GSM153174 2 0.0000 0.937 0.000 1.000
#> GSM153175 2 0.4562 0.919 0.096 0.904
#> GSM153176 2 0.5842 0.904 0.140 0.860
#> GSM153177 2 0.1184 0.940 0.016 0.984
#> GSM152931 2 0.4431 0.921 0.092 0.908
#> GSM152932 2 0.2423 0.940 0.040 0.960
#> GSM152933 2 0.0000 0.937 0.000 1.000
#> GSM152934 2 0.4939 0.919 0.108 0.892
#> GSM152935 2 0.4298 0.911 0.088 0.912
#> GSM152936 2 0.5178 0.914 0.116 0.884
#> GSM152937 2 0.4431 0.929 0.092 0.908
#> GSM152938 2 0.2948 0.929 0.052 0.948
#> GSM152939 2 0.3733 0.929 0.072 0.928
#> GSM152940 2 0.6623 0.882 0.172 0.828
#> GSM152941 1 0.9358 0.357 0.648 0.352
#> GSM152942 2 0.0672 0.939 0.008 0.992
#> GSM152943 2 0.5629 0.911 0.132 0.868
#> GSM152944 2 0.0000 0.937 0.000 1.000
#> GSM152945 2 0.4815 0.900 0.104 0.896
#> GSM152946 2 0.3733 0.931 0.072 0.928
#> GSM152947 2 0.7376 0.848 0.208 0.792
#> GSM152948 2 0.2423 0.940 0.040 0.960
#> GSM152949 2 0.0000 0.937 0.000 1.000
#> GSM152950 2 0.0000 0.937 0.000 1.000
#> GSM152951 2 0.2423 0.940 0.040 0.960
#> GSM152952 2 0.2603 0.940 0.044 0.956
#> GSM152953 2 0.2423 0.940 0.040 0.960
#> GSM152954 2 0.4939 0.917 0.108 0.892
#> GSM152955 2 0.4562 0.906 0.096 0.904
#> GSM152956 2 0.2423 0.940 0.040 0.960
#> GSM152957 2 0.6343 0.891 0.160 0.840
#> GSM152958 2 0.6148 0.897 0.152 0.848
#> GSM152959 2 0.5946 0.902 0.144 0.856
#> GSM152960 2 0.4562 0.919 0.096 0.904
#> GSM152961 2 0.6343 0.891 0.160 0.840
#> GSM152962 2 0.2948 0.929 0.052 0.948
#> GSM152963 2 0.2778 0.939 0.048 0.952
#> GSM152964 2 0.5059 0.895 0.112 0.888
#> GSM152965 2 0.2423 0.940 0.040 0.960
#> GSM152966 2 0.4431 0.921 0.092 0.908
#> GSM152967 2 0.2236 0.940 0.036 0.964
#> GSM152968 2 0.0000 0.937 0.000 1.000
#> GSM152969 2 0.4562 0.919 0.096 0.904
#> GSM152970 2 0.7376 0.848 0.208 0.792
#> GSM152971 2 0.4562 0.919 0.096 0.904
#> GSM152972 2 0.4939 0.917 0.108 0.892
#> GSM152973 2 0.3879 0.928 0.076 0.924
#> GSM152974 2 0.1184 0.940 0.016 0.984
#> GSM152975 2 0.3431 0.924 0.064 0.936
#> GSM152976 2 0.6048 0.899 0.148 0.852
#> GSM152977 2 0.6048 0.899 0.148 0.852
#> GSM152978 2 0.4562 0.919 0.096 0.904
#> GSM152979 2 0.0672 0.938 0.008 0.992
#> GSM152980 2 0.2423 0.940 0.040 0.960
#> GSM152981 2 0.5059 0.895 0.112 0.888
#> GSM152982 2 0.4431 0.921 0.092 0.908
#> GSM152983 2 0.4562 0.919 0.096 0.904
#> GSM152984 2 0.0938 0.940 0.012 0.988
#> GSM152985 2 0.8555 0.748 0.280 0.720
#> GSM152986 2 0.5946 0.902 0.144 0.856
#> GSM152987 1 0.9044 0.440 0.680 0.320
#> GSM152988 2 0.3733 0.929 0.072 0.928
#> GSM152989 2 0.8386 0.762 0.268 0.732
#> GSM152990 2 0.0000 0.937 0.000 1.000
#> GSM152991 2 0.2423 0.933 0.040 0.960
#> GSM187524 1 0.0000 0.974 1.000 0.000
#> GSM187525 1 0.0000 0.974 1.000 0.000
#> GSM187526 1 0.0000 0.974 1.000 0.000
#> GSM187527 1 0.0000 0.974 1.000 0.000
#> GSM152856 1 0.0000 0.974 1.000 0.000
#> GSM152857 1 0.0000 0.974 1.000 0.000
#> GSM152858 1 0.0000 0.974 1.000 0.000
#> GSM152859 1 0.0000 0.974 1.000 0.000
#> GSM152860 1 0.0000 0.974 1.000 0.000
#> GSM152861 1 0.0000 0.974 1.000 0.000
#> GSM152862 1 0.0000 0.974 1.000 0.000
#> GSM152863 1 0.0000 0.974 1.000 0.000
#> GSM152864 1 0.0000 0.974 1.000 0.000
#> GSM152865 1 0.0000 0.974 1.000 0.000
#> GSM152866 1 0.0000 0.974 1.000 0.000
#> GSM152867 1 0.0000 0.974 1.000 0.000
#> GSM152868 1 0.0000 0.974 1.000 0.000
#> GSM152869 1 0.0000 0.974 1.000 0.000
#> GSM152870 1 0.0000 0.974 1.000 0.000
#> GSM152871 1 0.0000 0.974 1.000 0.000
#> GSM152872 1 0.0000 0.974 1.000 0.000
#> GSM152873 1 0.0000 0.974 1.000 0.000
#> GSM152874 1 0.0000 0.974 1.000 0.000
#> GSM152875 1 0.0000 0.974 1.000 0.000
#> GSM152876 1 0.0000 0.974 1.000 0.000
#> GSM152877 1 0.0000 0.974 1.000 0.000
#> GSM152878 1 0.0000 0.974 1.000 0.000
#> GSM152879 1 0.0000 0.974 1.000 0.000
#> GSM152880 1 0.0000 0.974 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.6299 0.3721 0.000 0.524 0.476
#> GSM152805 3 0.6168 0.2009 0.000 0.412 0.588
#> GSM152806 2 0.6299 0.0513 0.000 0.524 0.476
#> GSM152807 3 0.4062 0.6977 0.000 0.164 0.836
#> GSM152808 2 0.6299 0.0513 0.000 0.524 0.476
#> GSM152809 3 0.4178 0.6835 0.000 0.172 0.828
#> GSM152810 2 0.6770 0.3419 0.044 0.692 0.264
#> GSM152811 2 0.6309 0.0156 0.000 0.504 0.496
#> GSM152812 3 0.3267 0.7669 0.000 0.116 0.884
#> GSM152813 3 0.2711 0.7981 0.000 0.088 0.912
#> GSM152814 3 0.0592 0.8392 0.000 0.012 0.988
#> GSM152815 3 0.3752 0.7303 0.000 0.144 0.856
#> GSM152816 3 0.4178 0.6525 0.000 0.172 0.828
#> GSM152817 2 0.6299 0.0513 0.000 0.524 0.476
#> GSM152818 2 0.6299 0.0513 0.000 0.524 0.476
#> GSM152819 3 0.0892 0.8298 0.000 0.020 0.980
#> GSM152820 3 0.1031 0.8355 0.000 0.024 0.976
#> GSM152821 3 0.0424 0.8391 0.000 0.008 0.992
#> GSM153115 2 0.5754 0.6583 0.004 0.700 0.296
#> GSM153116 3 0.5397 0.4911 0.000 0.280 0.720
#> GSM153117 3 0.3267 0.7182 0.000 0.116 0.884
#> GSM153118 3 0.0000 0.8368 0.000 0.000 1.000
#> GSM153119 2 0.6299 0.0513 0.000 0.524 0.476
#> GSM153120 2 0.6595 0.6184 0.076 0.744 0.180
#> GSM153121 3 0.2878 0.7776 0.000 0.096 0.904
#> GSM153122 2 0.6299 0.0513 0.000 0.524 0.476
#> GSM153123 3 0.0000 0.8368 0.000 0.000 1.000
#> GSM153124 2 0.5905 0.5894 0.000 0.648 0.352
#> GSM153125 2 0.5529 0.6583 0.000 0.704 0.296
#> GSM153126 3 0.4974 0.5127 0.000 0.236 0.764
#> GSM153127 3 0.3340 0.7625 0.000 0.120 0.880
#> GSM153128 3 0.5760 0.3596 0.000 0.328 0.672
#> GSM153129 3 0.0237 0.8381 0.000 0.004 0.996
#> GSM153130 3 0.2537 0.7953 0.000 0.080 0.920
#> GSM153131 3 0.4842 0.5386 0.000 0.224 0.776
#> GSM153132 3 0.0000 0.8368 0.000 0.000 1.000
#> GSM153133 3 0.0424 0.8391 0.000 0.008 0.992
#> GSM153134 3 0.0000 0.8368 0.000 0.000 1.000
#> GSM153135 3 0.3686 0.7362 0.000 0.140 0.860
#> GSM153136 2 0.5722 0.6603 0.004 0.704 0.292
#> GSM153137 3 0.4062 0.7032 0.000 0.164 0.836
#> GSM153138 3 0.1399 0.8358 0.004 0.028 0.968
#> GSM153139 3 0.1411 0.8309 0.000 0.036 0.964
#> GSM153140 3 0.1289 0.8349 0.000 0.032 0.968
#> GSM153141 3 0.3340 0.7625 0.000 0.120 0.880
#> GSM153142 2 0.6302 0.0439 0.000 0.520 0.480
#> GSM153143 3 0.3551 0.7507 0.000 0.132 0.868
#> GSM153144 3 0.1031 0.8375 0.000 0.024 0.976
#> GSM153145 2 0.6299 0.0513 0.000 0.524 0.476
#> GSM153146 3 0.0747 0.8389 0.000 0.016 0.984
#> GSM153147 3 0.1643 0.8331 0.000 0.044 0.956
#> GSM153148 3 0.2959 0.7832 0.000 0.100 0.900
#> GSM153149 3 0.0592 0.8392 0.000 0.012 0.988
#> GSM153150 2 0.5919 0.6585 0.012 0.712 0.276
#> GSM153151 3 0.0892 0.8412 0.000 0.020 0.980
#> GSM153152 3 0.0237 0.8381 0.000 0.004 0.996
#> GSM153153 3 0.0747 0.8389 0.000 0.016 0.984
#> GSM153154 3 0.1031 0.8343 0.000 0.024 0.976
#> GSM153155 3 0.0892 0.8379 0.000 0.020 0.980
#> GSM153156 3 0.3192 0.7566 0.000 0.112 0.888
#> GSM153157 2 0.6308 0.0212 0.000 0.508 0.492
#> GSM153158 3 0.4235 0.6315 0.000 0.176 0.824
#> GSM153159 2 0.6305 0.0360 0.000 0.516 0.484
#> GSM153160 3 0.3941 0.6872 0.000 0.156 0.844
#> GSM153161 3 0.3412 0.7575 0.000 0.124 0.876
#> GSM153162 3 0.1529 0.8316 0.000 0.040 0.960
#> GSM153163 3 0.2356 0.8061 0.000 0.072 0.928
#> GSM153164 3 0.3116 0.7298 0.000 0.108 0.892
#> GSM153165 3 0.1411 0.8301 0.000 0.036 0.964
#> GSM153166 3 0.0424 0.8391 0.000 0.008 0.992
#> GSM153167 3 0.0424 0.8391 0.000 0.008 0.992
#> GSM153168 2 0.6299 0.0513 0.000 0.524 0.476
#> GSM153169 3 0.4346 0.6366 0.000 0.184 0.816
#> GSM153170 3 0.0424 0.8375 0.000 0.008 0.992
#> GSM153171 2 0.5722 0.6603 0.004 0.704 0.292
#> GSM153172 3 0.0747 0.8389 0.000 0.016 0.984
#> GSM153173 3 0.1753 0.8228 0.000 0.048 0.952
#> GSM153174 3 0.1964 0.8316 0.000 0.056 0.944
#> GSM153175 2 0.5529 0.6583 0.000 0.704 0.296
#> GSM153176 2 0.5902 0.6451 0.004 0.680 0.316
#> GSM153177 3 0.0000 0.8368 0.000 0.000 1.000
#> GSM152931 2 0.5754 0.6583 0.004 0.700 0.296
#> GSM152932 3 0.0747 0.8389 0.000 0.016 0.984
#> GSM152933 3 0.0000 0.8368 0.000 0.000 1.000
#> GSM152934 2 0.6169 0.5972 0.004 0.636 0.360
#> GSM152935 3 0.4931 0.5865 0.000 0.232 0.768
#> GSM152936 2 0.5754 0.6587 0.004 0.700 0.296
#> GSM152937 3 0.5882 0.3280 0.000 0.348 0.652
#> GSM152938 3 0.4931 0.5376 0.000 0.232 0.768
#> GSM152939 2 0.5529 0.6583 0.000 0.704 0.296
#> GSM152940 2 0.6746 0.6232 0.076 0.732 0.192
#> GSM152941 2 0.6297 0.4926 0.184 0.756 0.060
#> GSM152942 3 0.5178 0.4846 0.000 0.256 0.744
#> GSM152943 2 0.6513 0.2918 0.004 0.520 0.476
#> GSM152944 3 0.0892 0.8354 0.000 0.020 0.980
#> GSM152945 2 0.6516 0.0451 0.004 0.516 0.480
#> GSM152946 3 0.4452 0.6407 0.000 0.192 0.808
#> GSM152947 2 0.7337 0.5918 0.140 0.708 0.152
#> GSM152948 3 0.4291 0.6678 0.000 0.180 0.820
#> GSM152949 3 0.1163 0.8338 0.000 0.028 0.972
#> GSM152950 3 0.0424 0.8391 0.000 0.008 0.992
#> GSM152951 3 0.3551 0.7481 0.000 0.132 0.868
#> GSM152952 3 0.3412 0.7575 0.000 0.124 0.876
#> GSM152953 3 0.3267 0.7673 0.000 0.116 0.884
#> GSM152954 2 0.5722 0.6603 0.004 0.704 0.292
#> GSM152955 2 0.6307 0.0289 0.000 0.512 0.488
#> GSM152956 3 0.3340 0.7625 0.000 0.120 0.880
#> GSM152957 2 0.5864 0.6602 0.008 0.704 0.288
#> GSM152958 2 0.5864 0.6602 0.008 0.704 0.288
#> GSM152959 2 0.5722 0.6603 0.004 0.704 0.292
#> GSM152960 2 0.5785 0.6560 0.004 0.696 0.300
#> GSM152961 2 0.6195 0.6571 0.020 0.704 0.276
#> GSM152962 3 0.3412 0.7577 0.000 0.124 0.876
#> GSM152963 3 0.3340 0.7625 0.000 0.120 0.880
#> GSM152964 2 0.6299 0.0513 0.000 0.524 0.476
#> GSM152965 3 0.0424 0.8391 0.000 0.008 0.992
#> GSM152966 2 0.5529 0.6583 0.000 0.704 0.296
#> GSM152967 3 0.3192 0.7715 0.000 0.112 0.888
#> GSM152968 3 0.0424 0.8390 0.000 0.008 0.992
#> GSM152969 2 0.5754 0.6583 0.004 0.700 0.296
#> GSM152970 2 0.7297 0.6140 0.108 0.704 0.188
#> GSM152971 2 0.5722 0.6603 0.004 0.704 0.292
#> GSM152972 2 0.5722 0.6603 0.004 0.704 0.292
#> GSM152973 2 0.5529 0.6583 0.000 0.704 0.296
#> GSM152974 3 0.0424 0.8391 0.000 0.008 0.992
#> GSM152975 3 0.4121 0.7266 0.000 0.168 0.832
#> GSM152976 2 0.5722 0.6603 0.004 0.704 0.292
#> GSM152977 2 0.5982 0.6337 0.004 0.668 0.328
#> GSM152978 2 0.5754 0.6583 0.004 0.700 0.296
#> GSM152979 3 0.3192 0.7727 0.000 0.112 0.888
#> GSM152980 3 0.3551 0.7654 0.000 0.132 0.868
#> GSM152981 2 0.6299 0.0513 0.000 0.524 0.476
#> GSM152982 2 0.5650 0.6470 0.000 0.688 0.312
#> GSM152983 2 0.5754 0.6583 0.004 0.700 0.296
#> GSM152984 3 0.6286 -0.2527 0.000 0.464 0.536
#> GSM152985 2 0.6561 0.5645 0.144 0.756 0.100
#> GSM152986 2 0.5722 0.6603 0.004 0.704 0.292
#> GSM152987 2 0.4682 0.4078 0.192 0.804 0.004
#> GSM152988 2 0.5529 0.6583 0.000 0.704 0.296
#> GSM152989 2 0.6781 0.6435 0.052 0.704 0.244
#> GSM152990 3 0.1529 0.8282 0.000 0.040 0.960
#> GSM152991 3 0.1964 0.8207 0.000 0.056 0.944
#> GSM187524 1 0.0237 0.9954 0.996 0.004 0.000
#> GSM187525 1 0.0237 0.9954 0.996 0.004 0.000
#> GSM187526 1 0.0424 0.9922 0.992 0.008 0.000
#> GSM187527 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152856 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152857 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152858 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152859 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152860 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152861 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152862 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152863 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152864 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152866 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152867 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152870 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152871 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152873 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152874 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152875 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152876 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152877 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152878 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152879 1 0.0000 0.9994 1.000 0.000 0.000
#> GSM152880 1 0.0000 0.9994 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.4406 0.561 0.000 0.700 0.000 0.300
#> GSM152805 2 0.4193 0.672 0.000 0.732 0.268 0.000
#> GSM152806 3 0.0592 0.892 0.000 0.016 0.984 0.000
#> GSM152807 2 0.1211 0.925 0.000 0.960 0.000 0.040
#> GSM152808 3 0.0592 0.892 0.000 0.016 0.984 0.000
#> GSM152809 2 0.1211 0.925 0.000 0.960 0.000 0.040
#> GSM152810 3 0.1022 0.869 0.000 0.000 0.968 0.032
#> GSM152811 3 0.1284 0.888 0.000 0.024 0.964 0.012
#> GSM152812 2 0.1022 0.928 0.000 0.968 0.000 0.032
#> GSM152813 2 0.1022 0.929 0.000 0.968 0.000 0.032
#> GSM152814 2 0.0921 0.929 0.000 0.972 0.000 0.028
#> GSM152815 2 0.1022 0.928 0.000 0.968 0.000 0.032
#> GSM152816 2 0.1584 0.918 0.000 0.952 0.036 0.012
#> GSM152817 3 0.0592 0.892 0.000 0.016 0.984 0.000
#> GSM152818 3 0.2760 0.834 0.000 0.128 0.872 0.000
#> GSM152819 2 0.1284 0.927 0.000 0.964 0.012 0.024
#> GSM152820 2 0.1004 0.929 0.000 0.972 0.004 0.024
#> GSM152821 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM153115 4 0.1474 0.951 0.000 0.052 0.000 0.948
#> GSM153116 3 0.4898 0.327 0.000 0.416 0.584 0.000
#> GSM153117 2 0.2921 0.842 0.000 0.860 0.140 0.000
#> GSM153118 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM153119 3 0.0592 0.892 0.000 0.016 0.984 0.000
#> GSM153120 4 0.1474 0.951 0.000 0.052 0.000 0.948
#> GSM153121 2 0.1807 0.904 0.000 0.940 0.008 0.052
#> GSM153122 3 0.0927 0.891 0.000 0.016 0.976 0.008
#> GSM153123 2 0.0592 0.929 0.000 0.984 0.000 0.016
#> GSM153124 4 0.4916 0.299 0.000 0.424 0.000 0.576
#> GSM153125 4 0.2149 0.921 0.000 0.088 0.000 0.912
#> GSM153126 2 0.2670 0.886 0.000 0.908 0.040 0.052
#> GSM153127 2 0.1022 0.928 0.000 0.968 0.000 0.032
#> GSM153128 3 0.4332 0.781 0.000 0.160 0.800 0.040
#> GSM153129 2 0.1211 0.912 0.000 0.960 0.000 0.040
#> GSM153130 2 0.2759 0.883 0.000 0.904 0.044 0.052
#> GSM153131 2 0.1624 0.921 0.000 0.952 0.028 0.020
#> GSM153132 2 0.0469 0.928 0.000 0.988 0.000 0.012
#> GSM153133 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM153134 2 0.1474 0.906 0.000 0.948 0.000 0.052
#> GSM153135 2 0.1118 0.927 0.000 0.964 0.000 0.036
#> GSM153136 4 0.1474 0.951 0.000 0.052 0.000 0.948
#> GSM153137 2 0.1576 0.919 0.000 0.948 0.004 0.048
#> GSM153138 2 0.2586 0.899 0.000 0.912 0.048 0.040
#> GSM153139 2 0.1661 0.905 0.000 0.944 0.004 0.052
#> GSM153140 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM153141 2 0.1022 0.928 0.000 0.968 0.000 0.032
#> GSM153142 3 0.1792 0.876 0.000 0.068 0.932 0.000
#> GSM153143 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM153144 2 0.1211 0.912 0.000 0.960 0.000 0.040
#> GSM153145 3 0.0592 0.892 0.000 0.016 0.984 0.000
#> GSM153146 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM153147 2 0.1474 0.906 0.000 0.948 0.000 0.052
#> GSM153148 2 0.1022 0.928 0.000 0.968 0.000 0.032
#> GSM153149 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM153150 4 0.1474 0.951 0.000 0.052 0.000 0.948
#> GSM153151 2 0.2816 0.885 0.000 0.900 0.064 0.036
#> GSM153152 2 0.0707 0.920 0.000 0.980 0.000 0.020
#> GSM153153 2 0.1022 0.928 0.000 0.968 0.000 0.032
#> GSM153154 2 0.1661 0.906 0.000 0.944 0.004 0.052
#> GSM153155 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM153156 2 0.2174 0.898 0.000 0.928 0.020 0.052
#> GSM153157 3 0.0592 0.892 0.000 0.016 0.984 0.000
#> GSM153158 2 0.3024 0.832 0.000 0.852 0.148 0.000
#> GSM153159 3 0.3486 0.776 0.000 0.188 0.812 0.000
#> GSM153160 2 0.2670 0.886 0.000 0.908 0.040 0.052
#> GSM153161 2 0.1118 0.927 0.000 0.964 0.000 0.036
#> GSM153162 2 0.1474 0.906 0.000 0.948 0.000 0.052
#> GSM153163 2 0.2578 0.889 0.000 0.912 0.036 0.052
#> GSM153164 2 0.2714 0.869 0.000 0.884 0.112 0.004
#> GSM153165 2 0.1661 0.905 0.000 0.944 0.004 0.052
#> GSM153166 2 0.0707 0.929 0.000 0.980 0.000 0.020
#> GSM153167 2 0.0592 0.929 0.000 0.984 0.000 0.016
#> GSM153168 3 0.0592 0.892 0.000 0.016 0.984 0.000
#> GSM153169 2 0.2759 0.885 0.000 0.904 0.044 0.052
#> GSM153170 2 0.1474 0.906 0.000 0.948 0.000 0.052
#> GSM153171 4 0.1474 0.951 0.000 0.052 0.000 0.948
#> GSM153172 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM153173 2 0.2385 0.894 0.000 0.920 0.028 0.052
#> GSM153174 2 0.1389 0.908 0.000 0.952 0.000 0.048
#> GSM153175 4 0.1474 0.946 0.000 0.052 0.000 0.948
#> GSM153176 4 0.1211 0.929 0.000 0.040 0.000 0.960
#> GSM153177 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM152931 4 0.1557 0.950 0.000 0.056 0.000 0.944
#> GSM152932 2 0.0921 0.929 0.000 0.972 0.000 0.028
#> GSM152933 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM152934 4 0.4805 0.782 0.000 0.132 0.084 0.784
#> GSM152935 2 0.5143 0.118 0.000 0.540 0.456 0.004
#> GSM152936 4 0.1637 0.947 0.000 0.060 0.000 0.940
#> GSM152937 3 0.3732 0.821 0.000 0.092 0.852 0.056
#> GSM152938 2 0.4259 0.813 0.000 0.816 0.128 0.056
#> GSM152939 4 0.1302 0.874 0.000 0.044 0.000 0.956
#> GSM152940 4 0.1722 0.948 0.008 0.048 0.000 0.944
#> GSM152941 4 0.2125 0.872 0.076 0.000 0.004 0.920
#> GSM152942 2 0.2473 0.893 0.000 0.908 0.012 0.080
#> GSM152943 3 0.6808 0.564 0.000 0.236 0.600 0.164
#> GSM152944 2 0.1474 0.906 0.000 0.948 0.000 0.052
#> GSM152945 3 0.2300 0.876 0.000 0.064 0.920 0.016
#> GSM152946 2 0.1302 0.923 0.000 0.956 0.000 0.044
#> GSM152947 4 0.1724 0.940 0.020 0.032 0.000 0.948
#> GSM152948 2 0.1118 0.927 0.000 0.964 0.000 0.036
#> GSM152949 2 0.1474 0.906 0.000 0.948 0.000 0.052
#> GSM152950 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM152951 2 0.1022 0.928 0.000 0.968 0.000 0.032
#> GSM152952 2 0.1118 0.927 0.000 0.964 0.000 0.036
#> GSM152953 2 0.1209 0.928 0.000 0.964 0.004 0.032
#> GSM152954 4 0.1474 0.951 0.000 0.052 0.000 0.948
#> GSM152955 3 0.3443 0.833 0.000 0.136 0.848 0.016
#> GSM152956 2 0.1118 0.927 0.000 0.964 0.000 0.036
#> GSM152957 4 0.1474 0.951 0.000 0.052 0.000 0.948
#> GSM152958 4 0.1474 0.951 0.000 0.052 0.000 0.948
#> GSM152959 4 0.1474 0.951 0.000 0.052 0.000 0.948
#> GSM152960 4 0.2915 0.913 0.000 0.080 0.028 0.892
#> GSM152961 4 0.1576 0.950 0.004 0.048 0.000 0.948
#> GSM152962 2 0.4104 0.780 0.000 0.808 0.164 0.028
#> GSM152963 2 0.1022 0.928 0.000 0.968 0.000 0.032
#> GSM152964 3 0.1182 0.888 0.000 0.016 0.968 0.016
#> GSM152965 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM152966 4 0.1716 0.945 0.000 0.064 0.000 0.936
#> GSM152967 2 0.0921 0.929 0.000 0.972 0.000 0.028
#> GSM152968 2 0.1474 0.906 0.000 0.948 0.000 0.052
#> GSM152969 4 0.1557 0.950 0.000 0.056 0.000 0.944
#> GSM152970 4 0.1733 0.936 0.024 0.028 0.000 0.948
#> GSM152971 4 0.1474 0.951 0.000 0.052 0.000 0.948
#> GSM152972 4 0.1474 0.951 0.000 0.052 0.000 0.948
#> GSM152973 4 0.1118 0.878 0.000 0.036 0.000 0.964
#> GSM152974 2 0.0817 0.929 0.000 0.976 0.000 0.024
#> GSM152975 2 0.3404 0.854 0.000 0.864 0.104 0.032
#> GSM152976 4 0.1474 0.951 0.000 0.052 0.000 0.948
#> GSM152977 4 0.1557 0.950 0.000 0.056 0.000 0.944
#> GSM152978 4 0.2882 0.912 0.000 0.084 0.024 0.892
#> GSM152979 2 0.2385 0.896 0.000 0.920 0.028 0.052
#> GSM152980 2 0.1211 0.925 0.000 0.960 0.000 0.040
#> GSM152981 3 0.0592 0.892 0.000 0.016 0.984 0.000
#> GSM152982 4 0.1557 0.950 0.000 0.056 0.000 0.944
#> GSM152983 4 0.1557 0.950 0.000 0.056 0.000 0.944
#> GSM152984 2 0.3569 0.777 0.000 0.804 0.000 0.196
#> GSM152985 4 0.2019 0.935 0.024 0.032 0.004 0.940
#> GSM152986 4 0.1474 0.951 0.000 0.052 0.000 0.948
#> GSM152987 4 0.2662 0.860 0.084 0.000 0.016 0.900
#> GSM152988 4 0.1211 0.875 0.000 0.040 0.000 0.960
#> GSM152989 4 0.1920 0.935 0.024 0.028 0.004 0.944
#> GSM152990 2 0.1661 0.905 0.000 0.944 0.004 0.052
#> GSM152991 2 0.5696 -0.127 0.000 0.492 0.484 0.024
#> GSM187524 1 0.1610 0.956 0.952 0.000 0.016 0.032
#> GSM187525 1 0.0779 0.985 0.980 0.000 0.016 0.004
#> GSM187526 1 0.0657 0.984 0.984 0.000 0.004 0.012
#> GSM187527 1 0.0524 0.987 0.988 0.000 0.004 0.008
#> GSM152856 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152857 1 0.0779 0.980 0.980 0.000 0.004 0.016
#> GSM152858 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152859 1 0.0592 0.987 0.984 0.000 0.016 0.000
#> GSM152860 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152861 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152862 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152863 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152864 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152866 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152867 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152868 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152870 1 0.0376 0.991 0.992 0.000 0.004 0.004
#> GSM152871 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152872 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152873 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152875 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152876 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152877 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152878 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152879 1 0.0000 0.995 1.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.995 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.3877 0.676 0.000 0.764 0.024 0.212 0.000
#> GSM152805 5 0.5405 0.353 0.000 0.076 0.328 0.000 0.596
#> GSM152806 5 0.0324 0.898 0.000 0.004 0.004 0.000 0.992
#> GSM152807 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM152808 5 0.0162 0.898 0.000 0.000 0.004 0.000 0.996
#> GSM152809 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM152810 5 0.1603 0.876 0.004 0.004 0.012 0.032 0.948
#> GSM152811 5 0.0865 0.891 0.000 0.000 0.024 0.004 0.972
#> GSM152812 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM152813 2 0.0324 0.932 0.000 0.992 0.004 0.004 0.000
#> GSM152814 2 0.0162 0.931 0.000 0.996 0.004 0.000 0.000
#> GSM152815 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM152816 3 0.3246 0.853 0.000 0.184 0.808 0.000 0.008
#> GSM152817 5 0.0162 0.898 0.000 0.000 0.004 0.000 0.996
#> GSM152818 5 0.0671 0.891 0.000 0.016 0.004 0.000 0.980
#> GSM152819 3 0.3508 0.808 0.000 0.252 0.748 0.000 0.000
#> GSM152820 3 0.3561 0.804 0.000 0.260 0.740 0.000 0.000
#> GSM152821 2 0.0162 0.931 0.000 0.996 0.004 0.000 0.000
#> GSM153115 4 0.1704 0.902 0.000 0.068 0.004 0.928 0.000
#> GSM153116 3 0.4660 0.717 0.000 0.080 0.728 0.000 0.192
#> GSM153117 3 0.3921 0.842 0.000 0.172 0.784 0.000 0.044
#> GSM153118 2 0.0162 0.931 0.000 0.996 0.004 0.000 0.000
#> GSM153119 5 0.0451 0.897 0.000 0.004 0.008 0.000 0.988
#> GSM153120 4 0.0162 0.908 0.000 0.000 0.004 0.996 0.000
#> GSM153121 3 0.2286 0.871 0.000 0.108 0.888 0.004 0.000
#> GSM153122 5 0.0404 0.897 0.000 0.000 0.012 0.000 0.988
#> GSM153123 2 0.1851 0.864 0.000 0.912 0.088 0.000 0.000
#> GSM153124 4 0.4510 0.288 0.000 0.432 0.008 0.560 0.000
#> GSM153125 4 0.3838 0.679 0.000 0.280 0.004 0.716 0.000
#> GSM153126 3 0.2629 0.867 0.000 0.104 0.880 0.004 0.012
#> GSM153127 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM153128 3 0.5479 0.732 0.000 0.128 0.724 0.068 0.080
#> GSM153129 2 0.3210 0.697 0.000 0.788 0.212 0.000 0.000
#> GSM153130 3 0.2411 0.871 0.000 0.108 0.884 0.000 0.008
#> GSM153131 3 0.2833 0.871 0.000 0.120 0.864 0.012 0.004
#> GSM153132 3 0.3932 0.726 0.000 0.328 0.672 0.000 0.000
#> GSM153133 2 0.0162 0.931 0.000 0.996 0.004 0.000 0.000
#> GSM153134 2 0.3210 0.703 0.000 0.788 0.212 0.000 0.000
#> GSM153135 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM153136 4 0.0566 0.913 0.000 0.012 0.004 0.984 0.000
#> GSM153137 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM153138 2 0.0613 0.928 0.000 0.984 0.004 0.008 0.004
#> GSM153139 3 0.2338 0.873 0.000 0.112 0.884 0.000 0.004
#> GSM153140 2 0.0162 0.931 0.000 0.996 0.004 0.000 0.000
#> GSM153141 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM153142 5 0.4558 0.505 0.000 0.024 0.324 0.000 0.652
#> GSM153143 2 0.0324 0.932 0.000 0.992 0.004 0.004 0.000
#> GSM153144 2 0.1197 0.899 0.000 0.952 0.048 0.000 0.000
#> GSM153145 5 0.0162 0.898 0.000 0.000 0.004 0.000 0.996
#> GSM153146 2 0.0324 0.932 0.000 0.992 0.004 0.004 0.000
#> GSM153147 3 0.3636 0.775 0.000 0.272 0.728 0.000 0.000
#> GSM153148 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM153149 2 0.0290 0.930 0.000 0.992 0.008 0.000 0.000
#> GSM153150 4 0.0451 0.911 0.000 0.004 0.008 0.988 0.000
#> GSM153151 2 0.1952 0.860 0.000 0.912 0.084 0.004 0.000
#> GSM153152 2 0.2179 0.840 0.000 0.888 0.112 0.000 0.000
#> GSM153153 2 0.0162 0.931 0.000 0.996 0.004 0.000 0.000
#> GSM153154 3 0.2280 0.873 0.000 0.120 0.880 0.000 0.000
#> GSM153155 2 0.0324 0.932 0.000 0.992 0.004 0.004 0.000
#> GSM153156 3 0.2230 0.873 0.000 0.116 0.884 0.000 0.000
#> GSM153157 5 0.2338 0.837 0.000 0.004 0.112 0.000 0.884
#> GSM153158 3 0.3543 0.847 0.000 0.112 0.828 0.000 0.060
#> GSM153159 5 0.4687 0.544 0.000 0.040 0.288 0.000 0.672
#> GSM153160 3 0.2731 0.866 0.000 0.104 0.876 0.004 0.016
#> GSM153161 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM153162 3 0.2929 0.852 0.000 0.180 0.820 0.000 0.000
#> GSM153163 3 0.2411 0.871 0.000 0.108 0.884 0.000 0.008
#> GSM153164 3 0.4687 0.678 0.000 0.336 0.636 0.000 0.028
#> GSM153165 3 0.2286 0.872 0.000 0.108 0.888 0.000 0.004
#> GSM153166 2 0.0703 0.920 0.000 0.976 0.024 0.000 0.000
#> GSM153167 2 0.3210 0.673 0.000 0.788 0.212 0.000 0.000
#> GSM153168 5 0.0162 0.898 0.000 0.000 0.004 0.000 0.996
#> GSM153169 3 0.2411 0.871 0.000 0.108 0.884 0.000 0.008
#> GSM153170 3 0.2280 0.873 0.000 0.120 0.880 0.000 0.000
#> GSM153171 4 0.0566 0.913 0.000 0.012 0.004 0.984 0.000
#> GSM153172 2 0.0162 0.931 0.000 0.996 0.004 0.000 0.000
#> GSM153173 3 0.2286 0.872 0.000 0.108 0.888 0.000 0.004
#> GSM153174 2 0.2424 0.816 0.000 0.868 0.132 0.000 0.000
#> GSM153175 4 0.2370 0.897 0.000 0.056 0.040 0.904 0.000
#> GSM153176 4 0.0740 0.912 0.000 0.008 0.008 0.980 0.004
#> GSM153177 2 0.0404 0.927 0.000 0.988 0.012 0.000 0.000
#> GSM152931 4 0.2233 0.879 0.000 0.104 0.004 0.892 0.000
#> GSM152932 2 0.0162 0.931 0.000 0.996 0.004 0.000 0.000
#> GSM152933 2 0.1121 0.903 0.000 0.956 0.044 0.000 0.000
#> GSM152934 4 0.2116 0.892 0.000 0.076 0.008 0.912 0.004
#> GSM152935 3 0.5987 0.569 0.000 0.324 0.544 0.000 0.132
#> GSM152936 4 0.1830 0.902 0.000 0.068 0.008 0.924 0.000
#> GSM152937 3 0.5763 0.594 0.000 0.040 0.680 0.184 0.096
#> GSM152938 3 0.4228 0.815 0.000 0.108 0.788 0.100 0.004
#> GSM152939 4 0.3112 0.859 0.000 0.044 0.100 0.856 0.000
#> GSM152940 4 0.0000 0.909 0.000 0.000 0.000 1.000 0.000
#> GSM152941 4 0.2582 0.856 0.024 0.000 0.080 0.892 0.004
#> GSM152942 3 0.2722 0.868 0.000 0.108 0.872 0.020 0.000
#> GSM152943 2 0.4960 0.406 0.000 0.616 0.016 0.352 0.016
#> GSM152944 3 0.2338 0.873 0.000 0.112 0.884 0.000 0.004
#> GSM152945 2 0.7479 -0.245 0.000 0.340 0.328 0.032 0.300
#> GSM152946 2 0.0451 0.931 0.000 0.988 0.004 0.008 0.000
#> GSM152947 4 0.0324 0.911 0.000 0.004 0.004 0.992 0.000
#> GSM152948 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM152949 3 0.2329 0.873 0.000 0.124 0.876 0.000 0.000
#> GSM152950 3 0.4242 0.537 0.000 0.428 0.572 0.000 0.000
#> GSM152951 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM152952 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM152953 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM152954 4 0.0671 0.914 0.000 0.016 0.004 0.980 0.000
#> GSM152955 3 0.5353 0.599 0.000 0.052 0.668 0.024 0.256
#> GSM152956 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM152957 4 0.0451 0.912 0.000 0.008 0.000 0.988 0.004
#> GSM152958 4 0.0290 0.913 0.000 0.008 0.000 0.992 0.000
#> GSM152959 4 0.0740 0.911 0.000 0.008 0.008 0.980 0.004
#> GSM152960 4 0.3365 0.801 0.000 0.180 0.008 0.808 0.004
#> GSM152961 4 0.0162 0.911 0.000 0.004 0.000 0.996 0.000
#> GSM152962 3 0.4165 0.828 0.000 0.208 0.756 0.032 0.004
#> GSM152963 2 0.0162 0.932 0.000 0.996 0.000 0.004 0.000
#> GSM152964 5 0.2783 0.827 0.000 0.004 0.116 0.012 0.868
#> GSM152965 2 0.0324 0.932 0.000 0.992 0.004 0.004 0.000
#> GSM152966 4 0.2763 0.843 0.000 0.148 0.004 0.848 0.000
#> GSM152967 2 0.0324 0.932 0.000 0.992 0.004 0.004 0.000
#> GSM152968 3 0.3143 0.842 0.000 0.204 0.796 0.000 0.000
#> GSM152969 4 0.2719 0.847 0.000 0.144 0.004 0.852 0.000
#> GSM152970 4 0.0324 0.911 0.000 0.004 0.004 0.992 0.000
#> GSM152971 4 0.1502 0.908 0.000 0.056 0.004 0.940 0.000
#> GSM152972 4 0.1502 0.908 0.000 0.056 0.004 0.940 0.000
#> GSM152973 4 0.2835 0.855 0.000 0.016 0.112 0.868 0.004
#> GSM152974 2 0.0162 0.931 0.000 0.996 0.004 0.000 0.000
#> GSM152975 2 0.5335 0.542 0.000 0.676 0.208 0.112 0.004
#> GSM152976 4 0.0290 0.912 0.000 0.008 0.000 0.992 0.000
#> GSM152977 4 0.0566 0.913 0.000 0.012 0.004 0.984 0.000
#> GSM152978 4 0.3243 0.805 0.000 0.180 0.004 0.812 0.004
#> GSM152979 3 0.2358 0.870 0.000 0.104 0.888 0.000 0.008
#> GSM152980 2 0.0451 0.931 0.000 0.988 0.004 0.008 0.000
#> GSM152981 5 0.0162 0.898 0.000 0.000 0.004 0.000 0.996
#> GSM152982 4 0.1628 0.908 0.000 0.056 0.008 0.936 0.000
#> GSM152983 4 0.1831 0.899 0.000 0.076 0.004 0.920 0.000
#> GSM152984 3 0.4981 0.698 0.000 0.120 0.708 0.172 0.000
#> GSM152985 4 0.1202 0.897 0.004 0.000 0.032 0.960 0.004
#> GSM152986 4 0.0671 0.914 0.000 0.016 0.004 0.980 0.000
#> GSM152987 4 0.3636 0.805 0.084 0.000 0.080 0.832 0.004
#> GSM152988 4 0.2932 0.858 0.000 0.032 0.104 0.864 0.000
#> GSM152989 4 0.1202 0.902 0.000 0.004 0.032 0.960 0.004
#> GSM152990 3 0.2230 0.873 0.000 0.116 0.884 0.000 0.000
#> GSM152991 3 0.4080 0.793 0.000 0.252 0.728 0.000 0.020
#> GSM187524 1 0.2189 0.939 0.904 0.000 0.084 0.012 0.000
#> GSM187525 1 0.2193 0.937 0.900 0.000 0.092 0.008 0.000
#> GSM187526 1 0.2193 0.937 0.900 0.000 0.092 0.008 0.000
#> GSM187527 1 0.0324 0.976 0.992 0.000 0.004 0.004 0.000
#> GSM152856 1 0.0162 0.978 0.996 0.000 0.004 0.000 0.000
#> GSM152857 1 0.0324 0.976 0.992 0.000 0.004 0.004 0.000
#> GSM152858 1 0.0510 0.974 0.984 0.000 0.016 0.000 0.000
#> GSM152859 1 0.1608 0.953 0.928 0.000 0.072 0.000 0.000
#> GSM152860 1 0.1830 0.951 0.924 0.000 0.068 0.008 0.000
#> GSM152861 1 0.0290 0.978 0.992 0.000 0.008 0.000 0.000
#> GSM152862 1 0.1638 0.955 0.932 0.000 0.064 0.004 0.000
#> GSM152863 1 0.0000 0.978 1.000 0.000 0.000 0.000 0.000
#> GSM152864 1 0.0162 0.978 0.996 0.000 0.004 0.000 0.000
#> GSM152865 1 0.0000 0.978 1.000 0.000 0.000 0.000 0.000
#> GSM152866 1 0.1410 0.958 0.940 0.000 0.060 0.000 0.000
#> GSM152867 1 0.0162 0.978 0.996 0.000 0.004 0.000 0.000
#> GSM152868 1 0.0162 0.978 0.996 0.000 0.004 0.000 0.000
#> GSM152869 1 0.0162 0.978 0.996 0.000 0.004 0.000 0.000
#> GSM152870 1 0.1956 0.947 0.916 0.000 0.076 0.008 0.000
#> GSM152871 1 0.0000 0.978 1.000 0.000 0.000 0.000 0.000
#> GSM152872 1 0.0963 0.968 0.964 0.000 0.036 0.000 0.000
#> GSM152873 1 0.0162 0.978 0.996 0.000 0.004 0.000 0.000
#> GSM152874 1 0.0290 0.978 0.992 0.000 0.008 0.000 0.000
#> GSM152875 1 0.0000 0.978 1.000 0.000 0.000 0.000 0.000
#> GSM152876 1 0.0000 0.978 1.000 0.000 0.000 0.000 0.000
#> GSM152877 1 0.0290 0.978 0.992 0.000 0.008 0.000 0.000
#> GSM152878 1 0.0162 0.978 0.996 0.000 0.004 0.000 0.000
#> GSM152879 1 0.0162 0.978 0.996 0.000 0.004 0.000 0.000
#> GSM152880 1 0.0162 0.978 0.996 0.000 0.004 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.4900 0.1845 0.000 0.548 0.040 0.400 0.000 0.012
#> GSM152805 5 0.4828 0.1373 0.000 0.004 0.468 0.008 0.492 0.028
#> GSM152806 5 0.0260 0.8630 0.000 0.000 0.008 0.000 0.992 0.000
#> GSM152807 2 0.2473 0.8100 0.000 0.856 0.008 0.000 0.000 0.136
#> GSM152808 5 0.0260 0.8630 0.000 0.000 0.008 0.000 0.992 0.000
#> GSM152809 2 0.2520 0.8017 0.000 0.844 0.004 0.000 0.000 0.152
#> GSM152810 5 0.4419 0.6692 0.000 0.000 0.004 0.132 0.728 0.136
#> GSM152811 5 0.1408 0.8470 0.000 0.000 0.020 0.036 0.944 0.000
#> GSM152812 2 0.2402 0.8062 0.000 0.856 0.004 0.000 0.000 0.140
#> GSM152813 2 0.0806 0.8301 0.000 0.972 0.020 0.000 0.000 0.008
#> GSM152814 2 0.0717 0.8306 0.000 0.976 0.016 0.000 0.000 0.008
#> GSM152815 2 0.2700 0.7984 0.000 0.836 0.004 0.004 0.000 0.156
#> GSM152816 3 0.2586 0.7869 0.000 0.096 0.876 0.004 0.004 0.020
#> GSM152817 5 0.0260 0.8630 0.000 0.000 0.008 0.000 0.992 0.000
#> GSM152818 5 0.0405 0.8623 0.000 0.004 0.008 0.000 0.988 0.000
#> GSM152819 3 0.3633 0.7189 0.000 0.252 0.732 0.004 0.000 0.012
#> GSM152820 3 0.3650 0.6881 0.000 0.280 0.708 0.000 0.000 0.012
#> GSM152821 2 0.1151 0.8262 0.000 0.956 0.032 0.000 0.000 0.012
#> GSM153115 4 0.1387 0.8698 0.000 0.068 0.000 0.932 0.000 0.000
#> GSM153116 3 0.5008 0.6978 0.000 0.096 0.700 0.008 0.176 0.020
#> GSM153117 3 0.4221 0.7606 0.000 0.172 0.756 0.004 0.052 0.016
#> GSM153118 2 0.1793 0.8218 0.000 0.928 0.036 0.000 0.004 0.032
#> GSM153119 5 0.0767 0.8629 0.000 0.000 0.012 0.008 0.976 0.004
#> GSM153120 4 0.1858 0.8619 0.000 0.004 0.000 0.904 0.000 0.092
#> GSM153121 3 0.0984 0.7865 0.000 0.008 0.968 0.012 0.000 0.012
#> GSM153122 5 0.0909 0.8600 0.000 0.000 0.012 0.020 0.968 0.000
#> GSM153123 2 0.2926 0.7873 0.000 0.844 0.124 0.000 0.004 0.028
#> GSM153124 4 0.3468 0.6295 0.000 0.284 0.004 0.712 0.000 0.000
#> GSM153125 4 0.2482 0.8180 0.000 0.148 0.004 0.848 0.000 0.000
#> GSM153126 3 0.1780 0.7725 0.000 0.004 0.932 0.036 0.004 0.024
#> GSM153127 2 0.2848 0.7944 0.000 0.828 0.004 0.008 0.000 0.160
#> GSM153128 3 0.6605 0.5373 0.000 0.124 0.552 0.240 0.064 0.020
#> GSM153129 2 0.4735 0.2342 0.000 0.568 0.384 0.000 0.004 0.044
#> GSM153130 3 0.1067 0.7788 0.000 0.004 0.964 0.004 0.004 0.024
#> GSM153131 3 0.2619 0.7951 0.000 0.072 0.880 0.040 0.000 0.008
#> GSM153132 3 0.4089 0.5575 0.000 0.352 0.632 0.000 0.004 0.012
#> GSM153133 2 0.1708 0.8217 0.000 0.932 0.040 0.000 0.004 0.024
#> GSM153134 2 0.4616 0.3161 0.000 0.576 0.384 0.000 0.004 0.036
#> GSM153135 2 0.2558 0.7999 0.000 0.840 0.004 0.000 0.000 0.156
#> GSM153136 4 0.1780 0.8767 0.000 0.048 0.000 0.924 0.000 0.028
#> GSM153137 2 0.4173 0.7237 0.000 0.748 0.012 0.180 0.000 0.060
#> GSM153138 2 0.3065 0.8053 0.000 0.848 0.048 0.096 0.000 0.008
#> GSM153139 3 0.1003 0.7956 0.000 0.028 0.964 0.004 0.000 0.004
#> GSM153140 2 0.0692 0.8299 0.000 0.976 0.020 0.000 0.000 0.004
#> GSM153141 2 0.2848 0.7944 0.000 0.828 0.004 0.008 0.000 0.160
#> GSM153142 5 0.3791 0.6899 0.000 0.004 0.224 0.008 0.748 0.016
#> GSM153143 2 0.1353 0.8317 0.000 0.952 0.024 0.012 0.000 0.012
#> GSM153144 2 0.1588 0.8190 0.000 0.924 0.072 0.000 0.000 0.004
#> GSM153145 5 0.0405 0.8639 0.000 0.000 0.008 0.004 0.988 0.000
#> GSM153146 2 0.1708 0.8311 0.000 0.932 0.024 0.000 0.004 0.040
#> GSM153147 3 0.3420 0.7481 0.000 0.204 0.776 0.008 0.000 0.012
#> GSM153148 2 0.2595 0.7980 0.000 0.836 0.004 0.000 0.000 0.160
#> GSM153149 2 0.2822 0.7753 0.000 0.856 0.108 0.000 0.004 0.032
#> GSM153150 4 0.1531 0.8650 0.000 0.004 0.000 0.928 0.000 0.068
#> GSM153151 2 0.5035 0.3241 0.000 0.596 0.332 0.056 0.000 0.016
#> GSM153152 2 0.4483 0.4369 0.000 0.636 0.320 0.000 0.004 0.040
#> GSM153153 2 0.1719 0.8269 0.000 0.932 0.032 0.000 0.004 0.032
#> GSM153154 3 0.1932 0.7986 0.000 0.076 0.912 0.004 0.004 0.004
#> GSM153155 2 0.1429 0.8222 0.000 0.940 0.052 0.004 0.000 0.004
#> GSM153156 3 0.0881 0.7890 0.000 0.012 0.972 0.008 0.000 0.008
#> GSM153157 5 0.2563 0.8078 0.000 0.004 0.108 0.008 0.872 0.008
#> GSM153158 3 0.3953 0.7731 0.000 0.128 0.792 0.008 0.060 0.012
#> GSM153159 5 0.3649 0.7198 0.000 0.004 0.204 0.008 0.768 0.016
#> GSM153160 3 0.1377 0.7758 0.000 0.004 0.952 0.016 0.004 0.024
#> GSM153161 2 0.2737 0.7964 0.000 0.832 0.004 0.004 0.000 0.160
#> GSM153162 3 0.2794 0.7800 0.000 0.144 0.840 0.004 0.000 0.012
#> GSM153163 3 0.1067 0.7788 0.000 0.004 0.964 0.004 0.004 0.024
#> GSM153164 3 0.4334 0.7209 0.000 0.232 0.716 0.004 0.032 0.016
#> GSM153165 3 0.0870 0.7885 0.000 0.012 0.972 0.004 0.000 0.012
#> GSM153166 2 0.3419 0.7098 0.000 0.792 0.176 0.000 0.004 0.028
#> GSM153167 2 0.3969 0.4088 0.000 0.652 0.332 0.000 0.000 0.016
#> GSM153168 5 0.0260 0.8630 0.000 0.000 0.008 0.000 0.992 0.000
#> GSM153169 3 0.1261 0.7794 0.000 0.004 0.956 0.008 0.004 0.028
#> GSM153170 3 0.1931 0.7964 0.000 0.068 0.916 0.004 0.004 0.008
#> GSM153171 4 0.1480 0.8763 0.000 0.040 0.000 0.940 0.000 0.020
#> GSM153172 2 0.0951 0.8305 0.000 0.968 0.020 0.000 0.004 0.008
#> GSM153173 3 0.1067 0.7788 0.000 0.004 0.964 0.004 0.004 0.024
#> GSM153174 2 0.3426 0.6979 0.000 0.764 0.220 0.004 0.000 0.012
#> GSM153175 4 0.1779 0.8689 0.000 0.064 0.016 0.920 0.000 0.000
#> GSM153176 4 0.2729 0.8592 0.000 0.008 0.032 0.876 0.004 0.080
#> GSM153177 2 0.3628 0.6813 0.000 0.776 0.184 0.000 0.004 0.036
#> GSM152931 4 0.1588 0.8683 0.000 0.072 0.004 0.924 0.000 0.000
#> GSM152932 2 0.1010 0.8263 0.000 0.960 0.036 0.000 0.000 0.004
#> GSM152933 2 0.3630 0.6949 0.000 0.780 0.176 0.000 0.004 0.040
#> GSM152934 4 0.2826 0.7939 0.000 0.128 0.028 0.844 0.000 0.000
#> GSM152935 3 0.5710 0.6969 0.000 0.188 0.652 0.028 0.108 0.024
#> GSM152936 4 0.0865 0.8757 0.000 0.036 0.000 0.964 0.000 0.000
#> GSM152937 3 0.6654 0.3600 0.000 0.040 0.468 0.360 0.100 0.032
#> GSM152938 3 0.4662 0.6798 0.000 0.100 0.700 0.192 0.000 0.008
#> GSM152939 4 0.2794 0.8403 0.000 0.060 0.080 0.860 0.000 0.000
#> GSM152940 4 0.2006 0.8577 0.000 0.004 0.000 0.892 0.000 0.104
#> GSM152941 4 0.3827 0.6983 0.008 0.000 0.000 0.680 0.004 0.308
#> GSM152942 3 0.3116 0.7289 0.000 0.016 0.836 0.132 0.004 0.012
#> GSM152943 4 0.4965 -0.1526 0.000 0.472 0.040 0.476 0.000 0.012
#> GSM152944 3 0.0858 0.7961 0.000 0.028 0.968 0.004 0.000 0.000
#> GSM152945 3 0.7952 0.1701 0.000 0.132 0.356 0.204 0.276 0.032
#> GSM152946 2 0.1713 0.8251 0.000 0.928 0.028 0.044 0.000 0.000
#> GSM152947 4 0.1908 0.8579 0.000 0.004 0.000 0.900 0.000 0.096
#> GSM152948 2 0.2308 0.8177 0.000 0.880 0.008 0.004 0.000 0.108
#> GSM152949 3 0.1788 0.7964 0.000 0.076 0.916 0.004 0.000 0.004
#> GSM152950 3 0.4129 0.4074 0.000 0.424 0.564 0.000 0.000 0.012
#> GSM152951 2 0.1908 0.8192 0.000 0.900 0.004 0.000 0.000 0.096
#> GSM152952 2 0.3037 0.7916 0.000 0.820 0.004 0.016 0.000 0.160
#> GSM152953 2 0.2611 0.8209 0.000 0.880 0.012 0.028 0.000 0.080
#> GSM152954 4 0.0260 0.8675 0.000 0.008 0.000 0.992 0.000 0.000
#> GSM152955 3 0.6833 0.3764 0.000 0.032 0.500 0.180 0.256 0.032
#> GSM152956 2 0.2737 0.7964 0.000 0.832 0.004 0.004 0.000 0.160
#> GSM152957 4 0.2600 0.8700 0.000 0.036 0.000 0.876 0.004 0.084
#> GSM152958 4 0.1594 0.8718 0.000 0.016 0.000 0.932 0.000 0.052
#> GSM152959 4 0.1897 0.8612 0.000 0.004 0.000 0.908 0.004 0.084
#> GSM152960 4 0.2001 0.8442 0.000 0.092 0.004 0.900 0.000 0.004
#> GSM152961 4 0.2060 0.8668 0.000 0.016 0.000 0.900 0.000 0.084
#> GSM152962 3 0.4626 0.7412 0.000 0.196 0.712 0.072 0.000 0.020
#> GSM152963 2 0.3336 0.7997 0.000 0.808 0.016 0.016 0.000 0.160
#> GSM152964 5 0.4103 0.6925 0.000 0.004 0.048 0.176 0.760 0.012
#> GSM152965 2 0.2119 0.8248 0.000 0.912 0.044 0.036 0.000 0.008
#> GSM152966 4 0.1812 0.8652 0.000 0.080 0.008 0.912 0.000 0.000
#> GSM152967 2 0.0858 0.8277 0.000 0.968 0.028 0.000 0.000 0.004
#> GSM152968 3 0.3855 0.6738 0.000 0.276 0.704 0.000 0.004 0.016
#> GSM152969 4 0.1958 0.8544 0.000 0.100 0.004 0.896 0.000 0.000
#> GSM152970 4 0.2100 0.8518 0.000 0.004 0.000 0.884 0.000 0.112
#> GSM152971 4 0.1141 0.8735 0.000 0.052 0.000 0.948 0.000 0.000
#> GSM152972 4 0.0865 0.8745 0.000 0.036 0.000 0.964 0.000 0.000
#> GSM152973 4 0.2642 0.8236 0.000 0.012 0.116 0.864 0.004 0.004
#> GSM152974 2 0.1176 0.8299 0.000 0.956 0.020 0.000 0.000 0.024
#> GSM152975 2 0.5567 0.4502 0.000 0.596 0.220 0.172 0.000 0.012
#> GSM152976 4 0.2308 0.8733 0.000 0.040 0.000 0.892 0.000 0.068
#> GSM152977 4 0.1728 0.8675 0.000 0.008 0.000 0.924 0.004 0.064
#> GSM152978 4 0.2544 0.8159 0.000 0.120 0.004 0.864 0.000 0.012
#> GSM152979 3 0.0964 0.7821 0.000 0.004 0.968 0.012 0.000 0.016
#> GSM152980 2 0.3576 0.7646 0.000 0.812 0.084 0.096 0.000 0.008
#> GSM152981 5 0.0260 0.8630 0.000 0.000 0.008 0.000 0.992 0.000
#> GSM152982 4 0.1204 0.8731 0.000 0.056 0.000 0.944 0.000 0.000
#> GSM152983 4 0.1327 0.8723 0.000 0.064 0.000 0.936 0.000 0.000
#> GSM152984 4 0.5355 -0.0438 0.000 0.092 0.452 0.452 0.000 0.004
#> GSM152985 4 0.3087 0.8114 0.004 0.004 0.000 0.804 0.004 0.184
#> GSM152986 4 0.1152 0.8741 0.000 0.044 0.000 0.952 0.000 0.004
#> GSM152987 4 0.4407 0.5847 0.024 0.000 0.000 0.592 0.004 0.380
#> GSM152988 4 0.2794 0.8403 0.000 0.060 0.080 0.860 0.000 0.000
#> GSM152989 4 0.2624 0.8336 0.000 0.004 0.000 0.844 0.004 0.148
#> GSM152990 3 0.0767 0.7889 0.000 0.012 0.976 0.004 0.000 0.008
#> GSM152991 3 0.4097 0.7076 0.000 0.256 0.712 0.008 0.008 0.016
#> GSM187524 6 0.3659 0.8958 0.364 0.000 0.000 0.000 0.000 0.636
#> GSM187525 6 0.3727 0.9177 0.388 0.000 0.000 0.000 0.000 0.612
#> GSM187526 6 0.3695 0.9121 0.376 0.000 0.000 0.000 0.000 0.624
#> GSM187527 1 0.1531 0.8166 0.928 0.000 0.004 0.000 0.000 0.068
#> GSM152856 1 0.0000 0.9105 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152857 1 0.2662 0.6504 0.840 0.000 0.004 0.004 0.000 0.152
#> GSM152858 1 0.0632 0.8903 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM152859 6 0.3828 0.8781 0.440 0.000 0.000 0.000 0.000 0.560
#> GSM152860 6 0.3862 0.8263 0.476 0.000 0.000 0.000 0.000 0.524
#> GSM152861 1 0.0146 0.9074 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM152862 1 0.3862 -0.7511 0.524 0.000 0.000 0.000 0.000 0.476
#> GSM152863 1 0.0508 0.9001 0.984 0.000 0.004 0.000 0.000 0.012
#> GSM152864 1 0.0000 0.9105 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.9105 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152866 1 0.3563 -0.2197 0.664 0.000 0.000 0.000 0.000 0.336
#> GSM152867 1 0.0000 0.9105 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152868 1 0.0000 0.9105 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.9105 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152870 6 0.3804 0.9054 0.424 0.000 0.000 0.000 0.000 0.576
#> GSM152871 1 0.0000 0.9105 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152872 1 0.0790 0.8799 0.968 0.000 0.000 0.000 0.000 0.032
#> GSM152873 1 0.0000 0.9105 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.9105 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152875 1 0.0260 0.9051 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM152876 1 0.0363 0.9015 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM152877 1 0.0000 0.9105 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152878 1 0.0000 0.9105 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152879 1 0.0000 0.9105 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.9105 1.000 0.000 0.000 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> CV:mclust 169 1.02e-30 2
#> CV:mclust 144 4.75e-29 3
#> CV:mclust 167 1.74e-33 4
#> CV:mclust 167 3.11e-33 5
#> CV:mclust 155 1.15e-30 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["CV", "NMF"]
# you can also extract it by
# res = res_list["CV:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'CV' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.927 0.939 0.974 0.4718 0.526 0.526
#> 3 3 0.469 0.622 0.807 0.3749 0.706 0.491
#> 4 4 0.499 0.536 0.749 0.1177 0.777 0.468
#> 5 5 0.557 0.621 0.758 0.0781 0.874 0.596
#> 6 6 0.604 0.539 0.732 0.0450 0.938 0.735
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.9803 0.000 1.000
#> GSM152805 2 0.0000 0.9803 0.000 1.000
#> GSM152806 2 0.0000 0.9803 0.000 1.000
#> GSM152807 2 0.0376 0.9772 0.004 0.996
#> GSM152808 2 0.0000 0.9803 0.000 1.000
#> GSM152809 2 0.0000 0.9803 0.000 1.000
#> GSM152810 1 0.0376 0.9590 0.996 0.004
#> GSM152811 2 0.0000 0.9803 0.000 1.000
#> GSM152812 2 0.0000 0.9803 0.000 1.000
#> GSM152813 2 0.0000 0.9803 0.000 1.000
#> GSM152814 2 0.0000 0.9803 0.000 1.000
#> GSM152815 2 0.0000 0.9803 0.000 1.000
#> GSM152816 2 0.0000 0.9803 0.000 1.000
#> GSM152817 2 0.0000 0.9803 0.000 1.000
#> GSM152818 2 0.0000 0.9803 0.000 1.000
#> GSM152819 2 0.0000 0.9803 0.000 1.000
#> GSM152820 2 0.0000 0.9803 0.000 1.000
#> GSM152821 2 0.0000 0.9803 0.000 1.000
#> GSM153115 1 0.6438 0.8136 0.836 0.164
#> GSM153116 2 0.0000 0.9803 0.000 1.000
#> GSM153117 2 0.0000 0.9803 0.000 1.000
#> GSM153118 2 0.0000 0.9803 0.000 1.000
#> GSM153119 2 0.0000 0.9803 0.000 1.000
#> GSM153120 1 0.0000 0.9610 1.000 0.000
#> GSM153121 2 0.0000 0.9803 0.000 1.000
#> GSM153122 2 0.2603 0.9397 0.044 0.956
#> GSM153123 2 0.0000 0.9803 0.000 1.000
#> GSM153124 2 0.7299 0.7358 0.204 0.796
#> GSM153125 2 0.7745 0.6932 0.228 0.772
#> GSM153126 2 0.0000 0.9803 0.000 1.000
#> GSM153127 2 0.0000 0.9803 0.000 1.000
#> GSM153128 2 0.6712 0.7749 0.176 0.824
#> GSM153129 2 0.0000 0.9803 0.000 1.000
#> GSM153130 2 0.0000 0.9803 0.000 1.000
#> GSM153131 2 0.0000 0.9803 0.000 1.000
#> GSM153132 2 0.0000 0.9803 0.000 1.000
#> GSM153133 2 0.0000 0.9803 0.000 1.000
#> GSM153134 2 0.0000 0.9803 0.000 1.000
#> GSM153135 2 0.0000 0.9803 0.000 1.000
#> GSM153136 1 0.7950 0.7069 0.760 0.240
#> GSM153137 1 0.3584 0.9137 0.932 0.068
#> GSM153138 2 0.0672 0.9738 0.008 0.992
#> GSM153139 2 0.0000 0.9803 0.000 1.000
#> GSM153140 2 0.0000 0.9803 0.000 1.000
#> GSM153141 2 0.1184 0.9670 0.016 0.984
#> GSM153142 2 0.0000 0.9803 0.000 1.000
#> GSM153143 2 0.0000 0.9803 0.000 1.000
#> GSM153144 2 0.0000 0.9803 0.000 1.000
#> GSM153145 2 0.0000 0.9803 0.000 1.000
#> GSM153146 2 0.0000 0.9803 0.000 1.000
#> GSM153147 2 0.0000 0.9803 0.000 1.000
#> GSM153148 2 0.0000 0.9803 0.000 1.000
#> GSM153149 2 0.0000 0.9803 0.000 1.000
#> GSM153150 1 0.0000 0.9610 1.000 0.000
#> GSM153151 2 0.0000 0.9803 0.000 1.000
#> GSM153152 2 0.0000 0.9803 0.000 1.000
#> GSM153153 2 0.0000 0.9803 0.000 1.000
#> GSM153154 2 0.0000 0.9803 0.000 1.000
#> GSM153155 2 0.0000 0.9803 0.000 1.000
#> GSM153156 2 0.0000 0.9803 0.000 1.000
#> GSM153157 2 0.0000 0.9803 0.000 1.000
#> GSM153158 2 0.0000 0.9803 0.000 1.000
#> GSM153159 2 0.0000 0.9803 0.000 1.000
#> GSM153160 2 0.0000 0.9803 0.000 1.000
#> GSM153161 2 0.0376 0.9772 0.004 0.996
#> GSM153162 2 0.0000 0.9803 0.000 1.000
#> GSM153163 2 0.0000 0.9803 0.000 1.000
#> GSM153164 2 0.0000 0.9803 0.000 1.000
#> GSM153165 2 0.0000 0.9803 0.000 1.000
#> GSM153166 2 0.0000 0.9803 0.000 1.000
#> GSM153167 2 0.0000 0.9803 0.000 1.000
#> GSM153168 2 0.0000 0.9803 0.000 1.000
#> GSM153169 2 0.0000 0.9803 0.000 1.000
#> GSM153170 2 0.0000 0.9803 0.000 1.000
#> GSM153171 1 0.0000 0.9610 1.000 0.000
#> GSM153172 2 0.0000 0.9803 0.000 1.000
#> GSM153173 2 0.0000 0.9803 0.000 1.000
#> GSM153174 2 0.0000 0.9803 0.000 1.000
#> GSM153175 2 0.9993 0.0118 0.484 0.516
#> GSM153176 1 0.6148 0.8275 0.848 0.152
#> GSM153177 2 0.0000 0.9803 0.000 1.000
#> GSM152931 1 0.7376 0.7548 0.792 0.208
#> GSM152932 2 0.0000 0.9803 0.000 1.000
#> GSM152933 2 0.0000 0.9803 0.000 1.000
#> GSM152934 1 0.4939 0.8750 0.892 0.108
#> GSM152935 2 0.0000 0.9803 0.000 1.000
#> GSM152936 1 0.0376 0.9590 0.996 0.004
#> GSM152937 1 0.9775 0.3369 0.588 0.412
#> GSM152938 2 0.2423 0.9436 0.040 0.960
#> GSM152939 2 0.0376 0.9772 0.004 0.996
#> GSM152940 1 0.0000 0.9610 1.000 0.000
#> GSM152941 1 0.0000 0.9610 1.000 0.000
#> GSM152942 2 0.0000 0.9803 0.000 1.000
#> GSM152943 1 0.0376 0.9589 0.996 0.004
#> GSM152944 2 0.0000 0.9803 0.000 1.000
#> GSM152945 1 0.9393 0.4812 0.644 0.356
#> GSM152946 2 0.1414 0.9632 0.020 0.980
#> GSM152947 1 0.0000 0.9610 1.000 0.000
#> GSM152948 2 0.0000 0.9803 0.000 1.000
#> GSM152949 2 0.0000 0.9803 0.000 1.000
#> GSM152950 2 0.0000 0.9803 0.000 1.000
#> GSM152951 2 0.0000 0.9803 0.000 1.000
#> GSM152952 2 0.0000 0.9803 0.000 1.000
#> GSM152953 2 0.0000 0.9803 0.000 1.000
#> GSM152954 1 0.1184 0.9520 0.984 0.016
#> GSM152955 2 0.0000 0.9803 0.000 1.000
#> GSM152956 2 0.0000 0.9803 0.000 1.000
#> GSM152957 1 0.0000 0.9610 1.000 0.000
#> GSM152958 1 0.0000 0.9610 1.000 0.000
#> GSM152959 1 0.0000 0.9610 1.000 0.000
#> GSM152960 1 0.0938 0.9546 0.988 0.012
#> GSM152961 1 0.0000 0.9610 1.000 0.000
#> GSM152962 2 0.0000 0.9803 0.000 1.000
#> GSM152963 2 0.0376 0.9772 0.004 0.996
#> GSM152964 1 0.8443 0.6525 0.728 0.272
#> GSM152965 2 0.0000 0.9803 0.000 1.000
#> GSM152966 2 1.0000 -0.0579 0.500 0.500
#> GSM152967 2 0.0000 0.9803 0.000 1.000
#> GSM152968 2 0.0000 0.9803 0.000 1.000
#> GSM152969 1 0.1184 0.9521 0.984 0.016
#> GSM152970 1 0.0000 0.9610 1.000 0.000
#> GSM152971 1 0.2423 0.9353 0.960 0.040
#> GSM152972 1 0.0000 0.9610 1.000 0.000
#> GSM152973 2 0.1633 0.9595 0.024 0.976
#> GSM152974 2 0.0000 0.9803 0.000 1.000
#> GSM152975 2 0.0000 0.9803 0.000 1.000
#> GSM152976 1 0.2778 0.9290 0.952 0.048
#> GSM152977 1 0.3274 0.9199 0.940 0.060
#> GSM152978 1 0.2236 0.9384 0.964 0.036
#> GSM152979 2 0.0000 0.9803 0.000 1.000
#> GSM152980 2 0.0376 0.9772 0.004 0.996
#> GSM152981 2 0.0000 0.9803 0.000 1.000
#> GSM152982 2 0.7056 0.7511 0.192 0.808
#> GSM152983 1 0.7528 0.7443 0.784 0.216
#> GSM152984 2 0.0000 0.9803 0.000 1.000
#> GSM152985 1 0.0000 0.9610 1.000 0.000
#> GSM152986 1 0.0000 0.9610 1.000 0.000
#> GSM152987 1 0.0000 0.9610 1.000 0.000
#> GSM152988 2 0.0376 0.9772 0.004 0.996
#> GSM152989 1 0.0000 0.9610 1.000 0.000
#> GSM152990 2 0.0000 0.9803 0.000 1.000
#> GSM152991 2 0.0000 0.9803 0.000 1.000
#> GSM187524 1 0.0000 0.9610 1.000 0.000
#> GSM187525 1 0.0000 0.9610 1.000 0.000
#> GSM187526 1 0.0000 0.9610 1.000 0.000
#> GSM187527 1 0.0000 0.9610 1.000 0.000
#> GSM152856 1 0.0000 0.9610 1.000 0.000
#> GSM152857 1 0.0000 0.9610 1.000 0.000
#> GSM152858 1 0.0000 0.9610 1.000 0.000
#> GSM152859 1 0.0000 0.9610 1.000 0.000
#> GSM152860 1 0.0000 0.9610 1.000 0.000
#> GSM152861 1 0.0000 0.9610 1.000 0.000
#> GSM152862 1 0.0000 0.9610 1.000 0.000
#> GSM152863 1 0.0000 0.9610 1.000 0.000
#> GSM152864 1 0.0000 0.9610 1.000 0.000
#> GSM152865 1 0.0000 0.9610 1.000 0.000
#> GSM152866 1 0.0000 0.9610 1.000 0.000
#> GSM152867 1 0.0000 0.9610 1.000 0.000
#> GSM152868 1 0.0000 0.9610 1.000 0.000
#> GSM152869 1 0.0000 0.9610 1.000 0.000
#> GSM152870 1 0.0000 0.9610 1.000 0.000
#> GSM152871 1 0.0000 0.9610 1.000 0.000
#> GSM152872 1 0.0000 0.9610 1.000 0.000
#> GSM152873 1 0.0000 0.9610 1.000 0.000
#> GSM152874 1 0.0000 0.9610 1.000 0.000
#> GSM152875 1 0.0000 0.9610 1.000 0.000
#> GSM152876 1 0.0000 0.9610 1.000 0.000
#> GSM152877 1 0.0000 0.9610 1.000 0.000
#> GSM152878 1 0.0000 0.9610 1.000 0.000
#> GSM152879 1 0.0000 0.9610 1.000 0.000
#> GSM152880 1 0.0000 0.9610 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.1289 0.6921 0.000 0.968 0.032
#> GSM152805 3 0.1643 0.7200 0.000 0.044 0.956
#> GSM152806 3 0.2096 0.7065 0.052 0.004 0.944
#> GSM152807 2 0.1267 0.6904 0.024 0.972 0.004
#> GSM152808 3 0.2165 0.7003 0.064 0.000 0.936
#> GSM152809 2 0.1711 0.6882 0.032 0.960 0.008
#> GSM152810 3 0.5560 0.4551 0.300 0.000 0.700
#> GSM152811 3 0.3851 0.6614 0.136 0.004 0.860
#> GSM152812 2 0.1182 0.6939 0.012 0.976 0.012
#> GSM152813 2 0.1643 0.6901 0.000 0.956 0.044
#> GSM152814 2 0.3192 0.6701 0.000 0.888 0.112
#> GSM152815 2 0.1491 0.6938 0.016 0.968 0.016
#> GSM152816 3 0.5785 0.5437 0.000 0.332 0.668
#> GSM152817 3 0.2537 0.6930 0.080 0.000 0.920
#> GSM152818 3 0.1315 0.7147 0.020 0.008 0.972
#> GSM152819 3 0.4504 0.6829 0.000 0.196 0.804
#> GSM152820 3 0.4974 0.6638 0.000 0.236 0.764
#> GSM152821 2 0.4654 0.6195 0.000 0.792 0.208
#> GSM153115 2 0.4796 0.4594 0.220 0.780 0.000
#> GSM153116 3 0.2625 0.7198 0.000 0.084 0.916
#> GSM153117 3 0.5497 0.5724 0.000 0.292 0.708
#> GSM153118 2 0.5560 0.5353 0.000 0.700 0.300
#> GSM153119 3 0.3116 0.6774 0.108 0.000 0.892
#> GSM153120 1 0.4861 0.8347 0.808 0.180 0.012
#> GSM153121 3 0.6111 0.4057 0.000 0.396 0.604
#> GSM153122 3 0.4235 0.6301 0.176 0.000 0.824
#> GSM153123 2 0.5497 0.5411 0.000 0.708 0.292
#> GSM153124 2 0.2772 0.6598 0.080 0.916 0.004
#> GSM153125 2 0.3482 0.6144 0.128 0.872 0.000
#> GSM153126 3 0.5397 0.6188 0.000 0.280 0.720
#> GSM153127 2 0.1774 0.6922 0.024 0.960 0.016
#> GSM153128 3 0.6488 0.6479 0.160 0.084 0.756
#> GSM153129 2 0.6026 0.3768 0.000 0.624 0.376
#> GSM153130 3 0.5016 0.6579 0.000 0.240 0.760
#> GSM153131 3 0.5254 0.6346 0.000 0.264 0.736
#> GSM153132 3 0.6079 0.4114 0.000 0.388 0.612
#> GSM153133 2 0.5497 0.5355 0.000 0.708 0.292
#> GSM153134 2 0.5465 0.5388 0.000 0.712 0.288
#> GSM153135 2 0.1751 0.6910 0.028 0.960 0.012
#> GSM153136 2 0.6244 -0.1973 0.440 0.560 0.000
#> GSM153137 2 0.7056 -0.0978 0.404 0.572 0.024
#> GSM153138 2 0.6521 0.0989 0.004 0.504 0.492
#> GSM153139 3 0.5529 0.5992 0.000 0.296 0.704
#> GSM153140 2 0.2537 0.6818 0.000 0.920 0.080
#> GSM153141 2 0.2599 0.6804 0.052 0.932 0.016
#> GSM153142 3 0.0747 0.7180 0.000 0.016 0.984
#> GSM153143 2 0.0983 0.6940 0.004 0.980 0.016
#> GSM153144 2 0.2796 0.6769 0.000 0.908 0.092
#> GSM153145 3 0.1525 0.7115 0.032 0.004 0.964
#> GSM153146 2 0.5621 0.5172 0.000 0.692 0.308
#> GSM153147 2 0.5968 0.4055 0.000 0.636 0.364
#> GSM153148 2 0.1182 0.6940 0.012 0.976 0.012
#> GSM153149 2 0.5926 0.4208 0.000 0.644 0.356
#> GSM153150 1 0.4589 0.8394 0.820 0.172 0.008
#> GSM153151 3 0.5905 0.5011 0.000 0.352 0.648
#> GSM153152 2 0.5835 0.4555 0.000 0.660 0.340
#> GSM153153 2 0.5254 0.5650 0.000 0.736 0.264
#> GSM153154 3 0.5465 0.6068 0.000 0.288 0.712
#> GSM153155 2 0.5016 0.5900 0.000 0.760 0.240
#> GSM153156 3 0.5397 0.6188 0.000 0.280 0.720
#> GSM153157 3 0.2384 0.7067 0.056 0.008 0.936
#> GSM153158 3 0.3941 0.7020 0.000 0.156 0.844
#> GSM153159 3 0.0747 0.7182 0.000 0.016 0.984
#> GSM153160 3 0.4887 0.6699 0.000 0.228 0.772
#> GSM153161 2 0.2492 0.6826 0.048 0.936 0.016
#> GSM153162 2 0.5465 0.5339 0.000 0.712 0.288
#> GSM153163 3 0.4555 0.6904 0.000 0.200 0.800
#> GSM153164 3 0.4504 0.6804 0.000 0.196 0.804
#> GSM153165 3 0.6260 0.2490 0.000 0.448 0.552
#> GSM153166 2 0.5431 0.5441 0.000 0.716 0.284
#> GSM153167 2 0.5706 0.4918 0.000 0.680 0.320
#> GSM153168 3 0.2796 0.6866 0.092 0.000 0.908
#> GSM153169 3 0.3551 0.7150 0.000 0.132 0.868
#> GSM153170 3 0.6302 0.1293 0.000 0.480 0.520
#> GSM153171 1 0.6045 0.6141 0.620 0.380 0.000
#> GSM153172 2 0.4178 0.6410 0.000 0.828 0.172
#> GSM153173 3 0.5706 0.5659 0.000 0.320 0.680
#> GSM153174 2 0.4291 0.6351 0.000 0.820 0.180
#> GSM153175 2 0.4233 0.5712 0.160 0.836 0.004
#> GSM153176 3 0.6931 0.2010 0.456 0.016 0.528
#> GSM153177 2 0.6180 0.2817 0.000 0.584 0.416
#> GSM152931 2 0.4654 0.4835 0.208 0.792 0.000
#> GSM152932 2 0.4452 0.6288 0.000 0.808 0.192
#> GSM152933 2 0.6252 0.1912 0.000 0.556 0.444
#> GSM152934 1 0.6902 0.6727 0.732 0.100 0.168
#> GSM152935 3 0.2537 0.7203 0.000 0.080 0.920
#> GSM152936 1 0.6518 0.3820 0.512 0.484 0.004
#> GSM152937 3 0.7698 0.5146 0.304 0.072 0.624
#> GSM152938 3 0.5406 0.6820 0.020 0.200 0.780
#> GSM152939 2 0.2590 0.6630 0.072 0.924 0.004
#> GSM152940 1 0.4755 0.8313 0.808 0.184 0.008
#> GSM152941 1 0.3459 0.8718 0.892 0.096 0.012
#> GSM152942 2 0.6305 -0.0343 0.000 0.516 0.484
#> GSM152943 1 0.4007 0.8564 0.880 0.084 0.036
#> GSM152944 3 0.5138 0.6504 0.000 0.252 0.748
#> GSM152945 3 0.4931 0.5935 0.212 0.004 0.784
#> GSM152946 2 0.1482 0.6938 0.020 0.968 0.012
#> GSM152947 1 0.2998 0.8750 0.916 0.068 0.016
#> GSM152948 2 0.1453 0.6913 0.024 0.968 0.008
#> GSM152949 2 0.6079 0.3461 0.000 0.612 0.388
#> GSM152950 3 0.6308 0.0772 0.000 0.492 0.508
#> GSM152951 2 0.1337 0.6935 0.016 0.972 0.012
#> GSM152952 2 0.2599 0.6805 0.052 0.932 0.016
#> GSM152953 2 0.2339 0.6908 0.012 0.940 0.048
#> GSM152954 1 0.5845 0.7120 0.688 0.308 0.004
#> GSM152955 3 0.1753 0.7066 0.048 0.000 0.952
#> GSM152956 2 0.1620 0.6921 0.024 0.964 0.012
#> GSM152957 1 0.4842 0.8001 0.776 0.224 0.000
#> GSM152958 1 0.5785 0.6859 0.668 0.332 0.000
#> GSM152959 1 0.3644 0.8632 0.872 0.124 0.004
#> GSM152960 1 0.6318 0.6436 0.636 0.356 0.008
#> GSM152961 1 0.5327 0.7586 0.728 0.272 0.000
#> GSM152962 3 0.4796 0.6758 0.000 0.220 0.780
#> GSM152963 2 0.1647 0.6934 0.004 0.960 0.036
#> GSM152964 3 0.5016 0.5539 0.240 0.000 0.760
#> GSM152965 2 0.5882 0.4588 0.000 0.652 0.348
#> GSM152966 2 0.4002 0.5689 0.160 0.840 0.000
#> GSM152967 2 0.2796 0.6788 0.000 0.908 0.092
#> GSM152968 2 0.6308 -0.0418 0.000 0.508 0.492
#> GSM152969 2 0.5678 0.2274 0.316 0.684 0.000
#> GSM152970 1 0.3755 0.8651 0.872 0.120 0.008
#> GSM152971 2 0.6008 0.0420 0.372 0.628 0.000
#> GSM152972 2 0.6299 -0.3156 0.476 0.524 0.000
#> GSM152973 2 0.3148 0.6920 0.036 0.916 0.048
#> GSM152974 2 0.4235 0.6389 0.000 0.824 0.176
#> GSM152975 2 0.6274 0.2606 0.000 0.544 0.456
#> GSM152976 1 0.6096 0.7342 0.704 0.280 0.016
#> GSM152977 3 0.6189 0.3682 0.364 0.004 0.632
#> GSM152978 1 0.6205 0.6781 0.656 0.336 0.008
#> GSM152979 3 0.3192 0.7169 0.000 0.112 0.888
#> GSM152980 2 0.6026 0.3786 0.000 0.624 0.376
#> GSM152981 3 0.2448 0.6950 0.076 0.000 0.924
#> GSM152982 2 0.7685 0.3211 0.052 0.564 0.384
#> GSM152983 2 0.6189 0.0851 0.364 0.632 0.004
#> GSM152984 2 0.5859 0.4478 0.000 0.656 0.344
#> GSM152985 1 0.1182 0.8663 0.976 0.012 0.012
#> GSM152986 1 0.6295 0.4326 0.528 0.472 0.000
#> GSM152987 1 0.1878 0.8447 0.952 0.004 0.044
#> GSM152988 2 0.1647 0.6846 0.036 0.960 0.004
#> GSM152989 1 0.4452 0.8256 0.808 0.192 0.000
#> GSM152990 3 0.5905 0.5082 0.000 0.352 0.648
#> GSM152991 3 0.2066 0.7230 0.000 0.060 0.940
#> GSM187524 1 0.2878 0.8020 0.904 0.000 0.096
#> GSM187525 1 0.1411 0.8485 0.964 0.000 0.036
#> GSM187526 1 0.0892 0.8574 0.980 0.000 0.020
#> GSM187527 1 0.2625 0.8725 0.916 0.084 0.000
#> GSM152856 1 0.3482 0.8619 0.872 0.128 0.000
#> GSM152857 1 0.2774 0.8231 0.920 0.008 0.072
#> GSM152858 1 0.0892 0.8553 0.980 0.000 0.020
#> GSM152859 1 0.3752 0.7529 0.856 0.000 0.144
#> GSM152860 1 0.1163 0.8530 0.972 0.000 0.028
#> GSM152861 1 0.0892 0.8702 0.980 0.020 0.000
#> GSM152862 1 0.1031 0.8542 0.976 0.000 0.024
#> GSM152863 1 0.1585 0.8533 0.964 0.008 0.028
#> GSM152864 1 0.2448 0.8727 0.924 0.076 0.000
#> GSM152865 1 0.0661 0.8613 0.988 0.004 0.008
#> GSM152866 1 0.1411 0.8488 0.964 0.000 0.036
#> GSM152867 1 0.3482 0.8616 0.872 0.128 0.000
#> GSM152868 1 0.3686 0.8564 0.860 0.140 0.000
#> GSM152869 1 0.2959 0.8695 0.900 0.100 0.000
#> GSM152870 1 0.1529 0.8461 0.960 0.000 0.040
#> GSM152871 1 0.0592 0.8672 0.988 0.012 0.000
#> GSM152872 1 0.0747 0.8567 0.984 0.000 0.016
#> GSM152873 1 0.1411 0.8722 0.964 0.036 0.000
#> GSM152874 1 0.1525 0.8721 0.964 0.032 0.004
#> GSM152875 1 0.0661 0.8646 0.988 0.008 0.004
#> GSM152876 1 0.3686 0.8576 0.860 0.140 0.000
#> GSM152877 1 0.1289 0.8722 0.968 0.032 0.000
#> GSM152878 1 0.2537 0.8726 0.920 0.080 0.000
#> GSM152879 1 0.2711 0.8713 0.912 0.088 0.000
#> GSM152880 1 0.2066 0.8734 0.940 0.060 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.6910 0.5013 0.076 0.628 0.260 0.036
#> GSM152805 3 0.2530 0.6728 0.000 0.000 0.888 0.112
#> GSM152806 3 0.4585 0.4826 0.000 0.000 0.668 0.332
#> GSM152807 2 0.1139 0.7356 0.008 0.972 0.008 0.012
#> GSM152808 3 0.4605 0.4764 0.000 0.000 0.664 0.336
#> GSM152809 2 0.0000 0.7346 0.000 1.000 0.000 0.000
#> GSM152810 4 0.4307 0.4638 0.024 0.000 0.192 0.784
#> GSM152811 3 0.5244 0.3561 0.012 0.000 0.600 0.388
#> GSM152812 2 0.0000 0.7346 0.000 1.000 0.000 0.000
#> GSM152813 2 0.4341 0.7027 0.020 0.820 0.136 0.024
#> GSM152814 2 0.4364 0.6692 0.004 0.792 0.180 0.024
#> GSM152815 2 0.0707 0.7306 0.000 0.980 0.000 0.020
#> GSM152816 3 0.2597 0.7103 0.004 0.084 0.904 0.008
#> GSM152817 3 0.4585 0.4821 0.000 0.000 0.668 0.332
#> GSM152818 3 0.3610 0.6210 0.000 0.000 0.800 0.200
#> GSM152819 3 0.3587 0.6919 0.000 0.052 0.860 0.088
#> GSM152820 3 0.3894 0.7032 0.000 0.068 0.844 0.088
#> GSM152821 2 0.1510 0.7360 0.000 0.956 0.028 0.016
#> GSM153115 1 0.7206 0.3261 0.580 0.308 0.068 0.044
#> GSM153116 3 0.4295 0.5923 0.000 0.008 0.752 0.240
#> GSM153117 3 0.3474 0.7023 0.000 0.068 0.868 0.064
#> GSM153118 2 0.3217 0.7122 0.000 0.860 0.128 0.012
#> GSM153119 4 0.4985 -0.0793 0.000 0.000 0.468 0.532
#> GSM153120 4 0.6546 0.1434 0.076 0.432 0.000 0.492
#> GSM153121 3 0.3725 0.6992 0.020 0.100 0.860 0.020
#> GSM153122 4 0.5277 -0.0551 0.008 0.000 0.460 0.532
#> GSM153123 2 0.3763 0.7050 0.000 0.832 0.144 0.024
#> GSM153124 2 0.4121 0.7182 0.064 0.848 0.072 0.016
#> GSM153125 2 0.3504 0.7240 0.048 0.880 0.056 0.016
#> GSM153126 3 0.3346 0.7044 0.028 0.060 0.888 0.024
#> GSM153127 2 0.1557 0.7217 0.000 0.944 0.000 0.056
#> GSM153128 4 0.3873 0.5401 0.000 0.060 0.096 0.844
#> GSM153129 3 0.4866 0.3019 0.000 0.404 0.596 0.000
#> GSM153130 3 0.2197 0.7153 0.000 0.048 0.928 0.024
#> GSM153131 3 0.2644 0.7183 0.000 0.060 0.908 0.032
#> GSM153132 3 0.4983 0.6009 0.000 0.272 0.704 0.024
#> GSM153133 2 0.2867 0.7225 0.000 0.884 0.104 0.012
#> GSM153134 3 0.5576 0.1522 0.000 0.444 0.536 0.020
#> GSM153135 2 0.1118 0.7267 0.000 0.964 0.000 0.036
#> GSM153136 2 0.5840 0.4239 0.348 0.612 0.004 0.036
#> GSM153137 2 0.4088 0.5649 0.004 0.764 0.000 0.232
#> GSM153138 2 0.4564 0.4421 0.000 0.672 0.000 0.328
#> GSM153139 3 0.3335 0.7071 0.000 0.120 0.860 0.020
#> GSM153140 2 0.3983 0.7031 0.008 0.828 0.144 0.020
#> GSM153141 2 0.1867 0.7122 0.000 0.928 0.000 0.072
#> GSM153142 3 0.3873 0.6000 0.000 0.000 0.772 0.228
#> GSM153143 2 0.0657 0.7351 0.000 0.984 0.004 0.012
#> GSM153144 2 0.4682 0.6495 0.008 0.764 0.208 0.020
#> GSM153145 3 0.4605 0.4794 0.000 0.000 0.664 0.336
#> GSM153146 2 0.1820 0.7334 0.000 0.944 0.020 0.036
#> GSM153147 3 0.5260 0.2203 0.004 0.424 0.568 0.004
#> GSM153148 2 0.0921 0.7299 0.000 0.972 0.000 0.028
#> GSM153149 2 0.3392 0.7103 0.000 0.856 0.124 0.020
#> GSM153150 4 0.7236 0.1779 0.144 0.396 0.000 0.460
#> GSM153151 2 0.6042 0.3034 0.000 0.580 0.052 0.368
#> GSM153152 2 0.4917 0.4582 0.000 0.656 0.336 0.008
#> GSM153153 2 0.3355 0.6956 0.000 0.836 0.160 0.004
#> GSM153154 3 0.1888 0.7184 0.000 0.044 0.940 0.016
#> GSM153155 2 0.2610 0.7312 0.000 0.900 0.088 0.012
#> GSM153156 3 0.3542 0.7068 0.000 0.120 0.852 0.028
#> GSM153157 3 0.4661 0.4571 0.000 0.000 0.652 0.348
#> GSM153158 3 0.3606 0.6712 0.000 0.024 0.844 0.132
#> GSM153159 3 0.3764 0.6108 0.000 0.000 0.784 0.216
#> GSM153160 3 0.2269 0.7095 0.008 0.032 0.932 0.028
#> GSM153161 2 0.2081 0.7060 0.000 0.916 0.000 0.084
#> GSM153162 3 0.5887 0.5178 0.016 0.272 0.672 0.040
#> GSM153163 3 0.1411 0.7088 0.000 0.020 0.960 0.020
#> GSM153164 3 0.3900 0.6907 0.000 0.072 0.844 0.084
#> GSM153165 3 0.3552 0.6886 0.000 0.128 0.848 0.024
#> GSM153166 2 0.5685 0.0886 0.000 0.516 0.460 0.024
#> GSM153167 3 0.5594 0.1022 0.000 0.460 0.520 0.020
#> GSM153168 3 0.4790 0.4049 0.000 0.000 0.620 0.380
#> GSM153169 3 0.2892 0.7093 0.000 0.036 0.896 0.068
#> GSM153170 3 0.3695 0.6783 0.000 0.156 0.828 0.016
#> GSM153171 2 0.7140 0.0640 0.404 0.464 0.000 0.132
#> GSM153172 2 0.3161 0.7176 0.000 0.864 0.124 0.012
#> GSM153173 3 0.2973 0.7032 0.000 0.096 0.884 0.020
#> GSM153174 2 0.5862 0.2717 0.004 0.560 0.408 0.028
#> GSM153175 1 0.7390 0.3891 0.616 0.224 0.112 0.048
#> GSM153176 3 0.6613 0.2316 0.344 0.000 0.560 0.096
#> GSM153177 2 0.4576 0.5674 0.000 0.728 0.260 0.012
#> GSM152931 2 0.4441 0.6839 0.136 0.816 0.020 0.028
#> GSM152932 2 0.3108 0.7211 0.000 0.872 0.112 0.016
#> GSM152933 2 0.4957 0.5002 0.000 0.684 0.300 0.016
#> GSM152934 4 0.5571 0.2411 0.024 0.396 0.000 0.580
#> GSM152935 4 0.7569 0.0801 0.000 0.196 0.368 0.436
#> GSM152936 2 0.4781 0.5569 0.036 0.752 0.000 0.212
#> GSM152937 4 0.4492 0.5363 0.012 0.080 0.084 0.824
#> GSM152938 4 0.7418 -0.0433 0.008 0.132 0.392 0.468
#> GSM152939 2 0.8557 0.2247 0.352 0.420 0.180 0.048
#> GSM152940 2 0.6842 -0.0919 0.100 0.464 0.000 0.436
#> GSM152941 4 0.7102 0.1161 0.304 0.156 0.000 0.540
#> GSM152942 3 0.4170 0.6815 0.016 0.124 0.832 0.028
#> GSM152943 4 0.5590 0.0912 0.020 0.456 0.000 0.524
#> GSM152944 3 0.1833 0.7142 0.000 0.032 0.944 0.024
#> GSM152945 4 0.3661 0.5297 0.008 0.088 0.040 0.864
#> GSM152946 2 0.1059 0.7373 0.000 0.972 0.016 0.012
#> GSM152947 4 0.6542 0.3267 0.196 0.168 0.000 0.636
#> GSM152948 2 0.1271 0.7355 0.008 0.968 0.012 0.012
#> GSM152949 3 0.4781 0.6177 0.000 0.212 0.752 0.036
#> GSM152950 2 0.5506 -0.0198 0.000 0.512 0.472 0.016
#> GSM152951 2 0.0376 0.7349 0.000 0.992 0.004 0.004
#> GSM152952 2 0.2011 0.7111 0.000 0.920 0.000 0.080
#> GSM152953 2 0.3172 0.6541 0.000 0.840 0.000 0.160
#> GSM152954 2 0.7114 0.2843 0.232 0.564 0.000 0.204
#> GSM152955 4 0.5047 0.2933 0.000 0.016 0.316 0.668
#> GSM152956 2 0.0817 0.7305 0.000 0.976 0.000 0.024
#> GSM152957 1 0.2060 0.7631 0.932 0.016 0.000 0.052
#> GSM152958 2 0.7146 0.2632 0.276 0.548 0.000 0.176
#> GSM152959 1 0.6658 0.2577 0.472 0.084 0.000 0.444
#> GSM152960 2 0.5013 0.4564 0.020 0.688 0.000 0.292
#> GSM152961 2 0.7460 0.0967 0.348 0.468 0.000 0.184
#> GSM152962 4 0.7677 0.1180 0.000 0.248 0.296 0.456
#> GSM152963 2 0.2973 0.6679 0.000 0.856 0.000 0.144
#> GSM152964 4 0.3726 0.4444 0.000 0.000 0.212 0.788
#> GSM152965 2 0.3942 0.5821 0.000 0.764 0.000 0.236
#> GSM152966 2 0.6163 0.5692 0.236 0.684 0.052 0.028
#> GSM152967 2 0.2727 0.7293 0.004 0.900 0.084 0.012
#> GSM152968 3 0.4252 0.6124 0.000 0.252 0.744 0.004
#> GSM152969 2 0.2966 0.7170 0.076 0.896 0.008 0.020
#> GSM152970 1 0.7282 0.1414 0.436 0.148 0.000 0.416
#> GSM152971 2 0.4597 0.6599 0.148 0.800 0.008 0.044
#> GSM152972 2 0.4127 0.6476 0.052 0.824 0.000 0.124
#> GSM152973 1 0.6268 0.4758 0.692 0.044 0.216 0.048
#> GSM152974 2 0.2928 0.7235 0.000 0.880 0.108 0.012
#> GSM152975 2 0.6791 0.4106 0.004 0.564 0.332 0.100
#> GSM152976 1 0.3801 0.7121 0.868 0.024 0.048 0.060
#> GSM152977 4 0.6946 0.2106 0.116 0.000 0.380 0.504
#> GSM152978 2 0.5254 0.4251 0.028 0.672 0.000 0.300
#> GSM152979 3 0.1743 0.6952 0.000 0.004 0.940 0.056
#> GSM152980 2 0.3894 0.7189 0.000 0.844 0.068 0.088
#> GSM152981 3 0.4898 0.3335 0.000 0.000 0.584 0.416
#> GSM152982 2 0.7154 0.0932 0.092 0.460 0.436 0.012
#> GSM152983 2 0.4347 0.6894 0.096 0.828 0.008 0.068
#> GSM152984 3 0.5378 0.5488 0.004 0.264 0.696 0.036
#> GSM152985 4 0.5815 0.1850 0.288 0.060 0.000 0.652
#> GSM152986 2 0.6186 0.3621 0.352 0.584 0.000 0.064
#> GSM152987 4 0.4875 0.3935 0.160 0.068 0.000 0.772
#> GSM152988 1 0.7236 0.4147 0.636 0.112 0.204 0.048
#> GSM152989 1 0.4595 0.6860 0.780 0.044 0.000 0.176
#> GSM152990 3 0.2888 0.7004 0.000 0.124 0.872 0.004
#> GSM152991 3 0.6834 0.2198 0.000 0.100 0.476 0.424
#> GSM187524 4 0.4228 0.3057 0.232 0.008 0.000 0.760
#> GSM187525 4 0.4543 0.1118 0.324 0.000 0.000 0.676
#> GSM187526 1 0.5163 0.3525 0.516 0.004 0.000 0.480
#> GSM187527 1 0.0657 0.7558 0.984 0.000 0.004 0.012
#> GSM152856 1 0.0779 0.7674 0.980 0.004 0.000 0.016
#> GSM152857 1 0.2111 0.7428 0.932 0.000 0.024 0.044
#> GSM152858 1 0.3569 0.7145 0.804 0.000 0.000 0.196
#> GSM152859 4 0.4222 0.2389 0.272 0.000 0.000 0.728
#> GSM152860 1 0.4994 0.3560 0.520 0.000 0.000 0.480
#> GSM152861 1 0.3123 0.7440 0.844 0.000 0.000 0.156
#> GSM152862 1 0.4961 0.4133 0.552 0.000 0.000 0.448
#> GSM152863 1 0.1635 0.7647 0.948 0.000 0.008 0.044
#> GSM152864 1 0.1637 0.7746 0.940 0.000 0.000 0.060
#> GSM152865 1 0.2081 0.7709 0.916 0.000 0.000 0.084
#> GSM152866 1 0.5000 0.3102 0.500 0.000 0.000 0.500
#> GSM152867 1 0.0376 0.7636 0.992 0.004 0.000 0.004
#> GSM152868 1 0.0336 0.7594 0.992 0.000 0.000 0.008
#> GSM152869 1 0.1302 0.7735 0.956 0.000 0.000 0.044
#> GSM152870 1 0.4999 0.3298 0.508 0.000 0.000 0.492
#> GSM152871 1 0.2345 0.7675 0.900 0.000 0.000 0.100
#> GSM152872 1 0.3942 0.6835 0.764 0.000 0.000 0.236
#> GSM152873 1 0.1940 0.7731 0.924 0.000 0.000 0.076
#> GSM152874 1 0.2921 0.7523 0.860 0.000 0.000 0.140
#> GSM152875 1 0.1792 0.7733 0.932 0.000 0.000 0.068
#> GSM152876 1 0.1543 0.7413 0.956 0.004 0.008 0.032
#> GSM152877 1 0.2647 0.7609 0.880 0.000 0.000 0.120
#> GSM152878 1 0.1302 0.7739 0.956 0.000 0.000 0.044
#> GSM152879 1 0.1557 0.7745 0.944 0.000 0.000 0.056
#> GSM152880 1 0.1940 0.7735 0.924 0.000 0.000 0.076
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.4983 0.7036 0.044 0.768 0.120 0.008 0.060
#> GSM152805 5 0.2833 0.7501 0.000 0.004 0.140 0.004 0.852
#> GSM152806 5 0.2438 0.7898 0.000 0.000 0.060 0.040 0.900
#> GSM152807 2 0.1059 0.7813 0.008 0.968 0.020 0.004 0.000
#> GSM152808 5 0.1211 0.7911 0.000 0.000 0.016 0.024 0.960
#> GSM152809 2 0.0960 0.7785 0.008 0.972 0.004 0.016 0.000
#> GSM152810 4 0.5273 0.5532 0.020 0.000 0.044 0.656 0.280
#> GSM152811 5 0.2037 0.7749 0.004 0.000 0.012 0.064 0.920
#> GSM152812 2 0.1200 0.7819 0.008 0.964 0.012 0.016 0.000
#> GSM152813 2 0.2521 0.7666 0.008 0.896 0.084 0.004 0.008
#> GSM152814 2 0.2809 0.7623 0.004 0.888 0.068 0.004 0.036
#> GSM152815 2 0.1488 0.7787 0.008 0.956 0.016 0.012 0.008
#> GSM152816 5 0.4829 0.6659 0.000 0.068 0.200 0.008 0.724
#> GSM152817 5 0.1211 0.7923 0.000 0.000 0.024 0.016 0.960
#> GSM152818 5 0.2233 0.7736 0.000 0.000 0.104 0.004 0.892
#> GSM152819 5 0.3812 0.7375 0.000 0.092 0.096 0.000 0.812
#> GSM152820 5 0.4350 0.7176 0.004 0.068 0.100 0.024 0.804
#> GSM152821 2 0.2095 0.7820 0.000 0.928 0.028 0.020 0.024
#> GSM153115 1 0.7495 0.0735 0.392 0.284 0.292 0.028 0.004
#> GSM153116 5 0.2610 0.7914 0.000 0.004 0.076 0.028 0.892
#> GSM153117 5 0.4137 0.7314 0.000 0.076 0.128 0.004 0.792
#> GSM153118 2 0.2954 0.7650 0.000 0.876 0.064 0.004 0.056
#> GSM153119 5 0.5258 0.4889 0.004 0.000 0.064 0.296 0.636
#> GSM153120 4 0.4798 0.6187 0.028 0.236 0.000 0.712 0.024
#> GSM153121 3 0.3716 0.6741 0.000 0.012 0.812 0.024 0.152
#> GSM153122 4 0.6346 0.4183 0.008 0.000 0.208 0.564 0.220
#> GSM153123 3 0.6582 0.1015 0.000 0.404 0.448 0.132 0.016
#> GSM153124 3 0.5394 0.3663 0.000 0.328 0.604 0.064 0.004
#> GSM153125 2 0.4704 0.6983 0.036 0.752 0.184 0.024 0.004
#> GSM153126 3 0.3360 0.6687 0.012 0.000 0.816 0.004 0.168
#> GSM153127 2 0.1329 0.7766 0.000 0.956 0.008 0.032 0.004
#> GSM153128 4 0.3952 0.6831 0.004 0.004 0.044 0.804 0.144
#> GSM153129 3 0.5996 0.5677 0.000 0.264 0.588 0.004 0.144
#> GSM153130 3 0.4318 0.5926 0.000 0.008 0.688 0.008 0.296
#> GSM153131 3 0.4928 0.4683 0.000 0.020 0.596 0.008 0.376
#> GSM153132 5 0.6056 0.3555 0.000 0.288 0.156 0.000 0.556
#> GSM153133 2 0.4291 0.7138 0.000 0.780 0.160 0.044 0.016
#> GSM153134 3 0.5630 0.5649 0.000 0.288 0.612 0.004 0.096
#> GSM153135 2 0.1282 0.7763 0.000 0.952 0.004 0.044 0.000
#> GSM153136 2 0.6033 0.4914 0.296 0.596 0.080 0.028 0.000
#> GSM153137 2 0.3863 0.6298 0.000 0.740 0.012 0.248 0.000
#> GSM153138 2 0.5156 0.2269 0.000 0.528 0.012 0.440 0.020
#> GSM153139 3 0.4790 0.5993 0.000 0.016 0.672 0.020 0.292
#> GSM153140 2 0.2795 0.7690 0.000 0.884 0.080 0.008 0.028
#> GSM153141 2 0.1809 0.7721 0.000 0.928 0.012 0.060 0.000
#> GSM153142 5 0.2077 0.7843 0.000 0.000 0.084 0.008 0.908
#> GSM153143 2 0.1314 0.7814 0.004 0.960 0.008 0.024 0.004
#> GSM153144 2 0.3719 0.6738 0.004 0.776 0.208 0.000 0.012
#> GSM153145 5 0.2376 0.7895 0.000 0.000 0.044 0.052 0.904
#> GSM153146 2 0.2529 0.7824 0.000 0.908 0.024 0.036 0.032
#> GSM153147 3 0.4696 0.6836 0.000 0.116 0.776 0.036 0.072
#> GSM153148 2 0.1484 0.7763 0.000 0.944 0.008 0.048 0.000
#> GSM153149 2 0.3688 0.7590 0.000 0.844 0.080 0.036 0.040
#> GSM153150 4 0.4181 0.6839 0.032 0.156 0.004 0.792 0.016
#> GSM153151 4 0.6354 0.5579 0.000 0.164 0.164 0.628 0.044
#> GSM153152 2 0.5950 -0.0776 0.000 0.468 0.448 0.012 0.072
#> GSM153153 2 0.3141 0.7426 0.000 0.852 0.040 0.000 0.108
#> GSM153154 5 0.3772 0.7113 0.000 0.036 0.172 0.000 0.792
#> GSM153155 2 0.2456 0.7819 0.000 0.904 0.064 0.024 0.008
#> GSM153156 3 0.4296 0.6655 0.000 0.024 0.756 0.016 0.204
#> GSM153157 5 0.2520 0.7800 0.000 0.000 0.048 0.056 0.896
#> GSM153158 5 0.3080 0.7620 0.000 0.020 0.124 0.004 0.852
#> GSM153159 5 0.3764 0.7389 0.000 0.000 0.156 0.044 0.800
#> GSM153160 3 0.3688 0.6671 0.008 0.000 0.808 0.024 0.160
#> GSM153161 2 0.2624 0.7524 0.000 0.872 0.012 0.116 0.000
#> GSM153162 3 0.4207 0.6936 0.008 0.084 0.808 0.008 0.092
#> GSM153163 3 0.4675 0.3165 0.000 0.004 0.544 0.008 0.444
#> GSM153164 5 0.3898 0.7191 0.000 0.116 0.080 0.000 0.804
#> GSM153165 3 0.4751 0.6250 0.000 0.036 0.692 0.008 0.264
#> GSM153166 2 0.5870 0.3042 0.000 0.584 0.276 0.000 0.140
#> GSM153167 3 0.5620 0.5487 0.000 0.296 0.608 0.004 0.092
#> GSM153168 5 0.2139 0.7859 0.000 0.000 0.032 0.052 0.916
#> GSM153169 3 0.4434 0.5250 0.000 0.004 0.640 0.008 0.348
#> GSM153170 3 0.4679 0.6623 0.000 0.056 0.720 0.004 0.220
#> GSM153171 3 0.8230 -0.0714 0.192 0.124 0.388 0.292 0.004
#> GSM153172 2 0.2460 0.7680 0.000 0.900 0.072 0.004 0.024
#> GSM153173 3 0.4653 0.5589 0.000 0.016 0.652 0.008 0.324
#> GSM153174 3 0.4397 0.5925 0.000 0.264 0.708 0.004 0.024
#> GSM153175 3 0.5376 0.5490 0.196 0.104 0.688 0.012 0.000
#> GSM153176 3 0.5568 0.5874 0.088 0.000 0.720 0.076 0.116
#> GSM153177 2 0.5006 0.6383 0.000 0.728 0.164 0.012 0.096
#> GSM152931 2 0.5262 0.6535 0.092 0.704 0.188 0.016 0.000
#> GSM152932 2 0.3307 0.7538 0.000 0.848 0.116 0.024 0.012
#> GSM152933 2 0.5309 0.5383 0.000 0.656 0.104 0.000 0.240
#> GSM152934 4 0.4385 0.7068 0.008 0.124 0.036 0.800 0.032
#> GSM152935 4 0.7091 0.4770 0.000 0.104 0.104 0.552 0.240
#> GSM152936 4 0.5799 0.0703 0.000 0.416 0.092 0.492 0.000
#> GSM152937 4 0.4312 0.6933 0.004 0.020 0.104 0.804 0.068
#> GSM152938 3 0.6232 0.1443 0.000 0.024 0.508 0.388 0.080
#> GSM152939 3 0.5483 0.5663 0.108 0.204 0.676 0.012 0.000
#> GSM152940 4 0.4143 0.6640 0.024 0.192 0.008 0.772 0.004
#> GSM152941 4 0.5646 0.5669 0.184 0.048 0.040 0.708 0.020
#> GSM152942 3 0.3610 0.6856 0.012 0.020 0.828 0.004 0.136
#> GSM152943 4 0.4038 0.7028 0.012 0.128 0.020 0.816 0.024
#> GSM152944 5 0.4754 0.4656 0.000 0.024 0.308 0.008 0.660
#> GSM152945 4 0.3816 0.7113 0.004 0.040 0.044 0.844 0.068
#> GSM152946 2 0.5531 0.5492 0.000 0.632 0.248 0.120 0.000
#> GSM152947 4 0.4025 0.7020 0.036 0.032 0.080 0.836 0.016
#> GSM152948 2 0.1211 0.7821 0.000 0.960 0.024 0.016 0.000
#> GSM152949 3 0.4254 0.6872 0.000 0.064 0.776 0.004 0.156
#> GSM152950 3 0.7116 0.4582 0.000 0.312 0.484 0.044 0.160
#> GSM152951 2 0.1493 0.7811 0.000 0.948 0.024 0.028 0.000
#> GSM152952 2 0.2052 0.7659 0.000 0.912 0.004 0.080 0.004
#> GSM152953 2 0.2733 0.7546 0.000 0.872 0.012 0.112 0.004
#> GSM152954 2 0.8229 0.2470 0.228 0.456 0.120 0.180 0.016
#> GSM152955 5 0.4697 0.3249 0.000 0.008 0.012 0.360 0.620
#> GSM152956 2 0.1408 0.7758 0.000 0.948 0.008 0.044 0.000
#> GSM152957 1 0.5951 0.4203 0.540 0.004 0.352 0.104 0.000
#> GSM152958 2 0.6783 0.4220 0.248 0.568 0.056 0.128 0.000
#> GSM152959 4 0.6843 0.4867 0.180 0.040 0.160 0.604 0.016
#> GSM152960 2 0.4990 0.4014 0.008 0.596 0.016 0.376 0.004
#> GSM152961 2 0.7593 0.1429 0.320 0.428 0.068 0.184 0.000
#> GSM152962 4 0.6653 0.4852 0.000 0.072 0.236 0.592 0.100
#> GSM152963 2 0.2352 0.7604 0.000 0.896 0.008 0.092 0.004
#> GSM152964 4 0.4164 0.5906 0.008 0.000 0.012 0.728 0.252
#> GSM152965 2 0.5180 0.4918 0.000 0.628 0.032 0.324 0.016
#> GSM152966 2 0.5446 0.6812 0.120 0.716 0.136 0.024 0.004
#> GSM152967 2 0.1981 0.7779 0.000 0.920 0.064 0.000 0.016
#> GSM152968 3 0.5497 0.6441 0.000 0.136 0.664 0.004 0.196
#> GSM152969 2 0.4887 0.7149 0.088 0.776 0.084 0.048 0.004
#> GSM152970 4 0.5538 0.5878 0.128 0.024 0.152 0.696 0.000
#> GSM152971 2 0.5883 0.6552 0.132 0.688 0.136 0.040 0.004
#> GSM152972 2 0.4351 0.7154 0.020 0.792 0.036 0.144 0.008
#> GSM152973 3 0.4117 0.5748 0.208 0.008 0.764 0.008 0.012
#> GSM152974 2 0.3774 0.7233 0.000 0.804 0.160 0.028 0.008
#> GSM152975 2 0.5597 0.3697 0.000 0.556 0.052 0.012 0.380
#> GSM152976 1 0.6491 0.3333 0.516 0.044 0.372 0.064 0.004
#> GSM152977 5 0.6650 0.4490 0.084 0.004 0.132 0.148 0.632
#> GSM152978 2 0.5863 0.6033 0.036 0.688 0.080 0.184 0.012
#> GSM152979 3 0.4152 0.5846 0.000 0.000 0.692 0.012 0.296
#> GSM152980 2 0.6486 0.6048 0.004 0.648 0.108 0.088 0.152
#> GSM152981 5 0.2570 0.7675 0.000 0.000 0.028 0.084 0.888
#> GSM152982 3 0.6040 0.5817 0.008 0.152 0.688 0.064 0.088
#> GSM152983 2 0.6642 0.5963 0.056 0.624 0.184 0.128 0.008
#> GSM152984 3 0.3689 0.6932 0.000 0.068 0.836 0.012 0.084
#> GSM152985 4 0.6686 0.5237 0.164 0.024 0.092 0.648 0.072
#> GSM152986 2 0.5946 0.5129 0.288 0.608 0.076 0.028 0.000
#> GSM152987 4 0.2244 0.6954 0.040 0.016 0.000 0.920 0.024
#> GSM152988 3 0.4946 0.5340 0.236 0.056 0.700 0.004 0.004
#> GSM152989 1 0.5749 0.6156 0.644 0.020 0.092 0.244 0.000
#> GSM152990 3 0.3669 0.6787 0.000 0.012 0.800 0.012 0.176
#> GSM152991 5 0.6129 0.5418 0.000 0.088 0.052 0.220 0.640
#> GSM187524 4 0.5048 0.6083 0.112 0.000 0.052 0.756 0.080
#> GSM187525 4 0.6111 0.4877 0.200 0.004 0.064 0.660 0.072
#> GSM187526 1 0.6523 0.2536 0.476 0.008 0.068 0.416 0.032
#> GSM187527 1 0.1211 0.7865 0.960 0.000 0.024 0.016 0.000
#> GSM152856 1 0.1059 0.7865 0.968 0.004 0.008 0.020 0.000
#> GSM152857 1 0.1646 0.7802 0.944 0.000 0.032 0.020 0.004
#> GSM152858 1 0.4355 0.7279 0.776 0.000 0.068 0.148 0.008
#> GSM152859 4 0.6231 0.5415 0.164 0.000 0.072 0.656 0.108
#> GSM152860 1 0.6625 0.3719 0.516 0.000 0.076 0.352 0.056
#> GSM152861 1 0.3037 0.7734 0.864 0.000 0.032 0.100 0.004
#> GSM152862 1 0.6443 0.5066 0.580 0.000 0.080 0.284 0.056
#> GSM152863 1 0.2075 0.7929 0.924 0.000 0.032 0.040 0.004
#> GSM152864 1 0.1444 0.7938 0.948 0.000 0.012 0.040 0.000
#> GSM152865 1 0.2419 0.7889 0.904 0.000 0.028 0.064 0.004
#> GSM152866 1 0.4907 0.1679 0.488 0.000 0.024 0.488 0.000
#> GSM152867 1 0.0671 0.7856 0.980 0.000 0.016 0.004 0.000
#> GSM152868 1 0.0898 0.7852 0.972 0.000 0.020 0.008 0.000
#> GSM152869 1 0.1243 0.7938 0.960 0.000 0.008 0.028 0.004
#> GSM152870 1 0.6852 0.3329 0.488 0.000 0.080 0.364 0.068
#> GSM152871 1 0.3611 0.7675 0.844 0.000 0.064 0.076 0.016
#> GSM152872 1 0.5052 0.6979 0.736 0.000 0.084 0.156 0.024
#> GSM152873 1 0.1981 0.7908 0.920 0.000 0.016 0.064 0.000
#> GSM152874 1 0.3441 0.7548 0.824 0.000 0.024 0.148 0.004
#> GSM152875 1 0.2650 0.7866 0.892 0.000 0.036 0.068 0.004
#> GSM152876 1 0.2053 0.7634 0.924 0.000 0.048 0.024 0.004
#> GSM152877 1 0.2228 0.7898 0.908 0.000 0.012 0.076 0.004
#> GSM152878 1 0.2313 0.7843 0.912 0.000 0.044 0.040 0.004
#> GSM152879 1 0.0771 0.7921 0.976 0.000 0.004 0.020 0.000
#> GSM152880 1 0.1168 0.7937 0.960 0.000 0.008 0.032 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.5677 0.58573 0.032 0.692 0.080 0.120 0.076 0.000
#> GSM152805 5 0.1876 0.80260 0.000 0.004 0.072 0.004 0.916 0.004
#> GSM152806 5 0.1477 0.80670 0.000 0.004 0.048 0.000 0.940 0.008
#> GSM152807 2 0.1225 0.71719 0.004 0.956 0.004 0.032 0.000 0.004
#> GSM152808 5 0.1503 0.80417 0.000 0.000 0.032 0.016 0.944 0.008
#> GSM152809 2 0.1285 0.71090 0.004 0.944 0.000 0.052 0.000 0.000
#> GSM152810 6 0.6589 0.25976 0.024 0.000 0.008 0.296 0.220 0.452
#> GSM152811 5 0.2918 0.76823 0.000 0.000 0.020 0.084 0.864 0.032
#> GSM152812 2 0.1439 0.72237 0.012 0.952 0.000 0.012 0.008 0.016
#> GSM152813 2 0.2312 0.71215 0.000 0.896 0.080 0.012 0.008 0.004
#> GSM152814 2 0.1659 0.72007 0.004 0.940 0.036 0.004 0.012 0.004
#> GSM152815 2 0.0810 0.72207 0.004 0.976 0.000 0.008 0.008 0.004
#> GSM152816 5 0.5257 0.65782 0.004 0.064 0.168 0.072 0.692 0.000
#> GSM152817 5 0.1515 0.80238 0.000 0.000 0.028 0.020 0.944 0.008
#> GSM152818 5 0.1364 0.80591 0.000 0.000 0.048 0.004 0.944 0.004
#> GSM152819 5 0.3364 0.76745 0.004 0.100 0.040 0.012 0.840 0.004
#> GSM152820 5 0.5688 0.45312 0.000 0.084 0.024 0.312 0.572 0.008
#> GSM152821 2 0.2649 0.72109 0.000 0.892 0.020 0.008 0.032 0.048
#> GSM153115 4 0.7242 0.21768 0.112 0.168 0.316 0.400 0.004 0.000
#> GSM153116 5 0.1911 0.80335 0.000 0.036 0.020 0.004 0.928 0.012
#> GSM153117 5 0.2750 0.78392 0.000 0.080 0.048 0.004 0.868 0.000
#> GSM153118 2 0.3348 0.70602 0.000 0.848 0.052 0.008 0.072 0.020
#> GSM153119 5 0.5260 0.16906 0.004 0.008 0.044 0.008 0.516 0.420
#> GSM153120 6 0.4712 0.53948 0.024 0.196 0.000 0.048 0.012 0.720
#> GSM153121 3 0.3303 0.73066 0.000 0.020 0.848 0.004 0.068 0.060
#> GSM153122 6 0.5044 0.54190 0.008 0.004 0.192 0.008 0.100 0.688
#> GSM153123 2 0.6822 -0.07101 0.004 0.328 0.324 0.016 0.008 0.320
#> GSM153124 3 0.6352 0.20202 0.000 0.156 0.504 0.300 0.004 0.036
#> GSM153125 2 0.5616 0.15463 0.008 0.488 0.084 0.412 0.004 0.004
#> GSM153126 3 0.1932 0.73138 0.000 0.000 0.924 0.020 0.040 0.016
#> GSM153127 2 0.1478 0.71903 0.000 0.944 0.000 0.032 0.004 0.020
#> GSM153128 6 0.4560 0.60228 0.012 0.012 0.060 0.088 0.044 0.784
#> GSM153129 3 0.5660 0.59979 0.000 0.196 0.648 0.072 0.080 0.004
#> GSM153130 3 0.3728 0.65595 0.000 0.008 0.748 0.004 0.228 0.012
#> GSM153131 3 0.5258 0.53710 0.000 0.048 0.624 0.024 0.292 0.012
#> GSM153132 5 0.5809 0.32391 0.000 0.344 0.140 0.012 0.504 0.000
#> GSM153133 2 0.4188 0.66126 0.000 0.756 0.140 0.008 0.000 0.096
#> GSM153134 3 0.5522 0.56961 0.000 0.256 0.620 0.012 0.096 0.016
#> GSM153135 2 0.1080 0.72276 0.004 0.960 0.000 0.004 0.000 0.032
#> GSM153136 2 0.6493 0.00428 0.088 0.440 0.056 0.404 0.004 0.008
#> GSM153137 2 0.4612 0.46663 0.000 0.636 0.000 0.052 0.004 0.308
#> GSM153138 2 0.5392 0.16784 0.000 0.496 0.000 0.088 0.008 0.408
#> GSM153139 3 0.4984 0.61038 0.000 0.044 0.672 0.012 0.248 0.024
#> GSM153140 2 0.5089 0.46456 0.000 0.632 0.064 0.280 0.024 0.000
#> GSM153141 2 0.1807 0.71569 0.000 0.920 0.000 0.020 0.000 0.060
#> GSM153142 5 0.1723 0.80690 0.000 0.004 0.048 0.012 0.932 0.004
#> GSM153143 2 0.1707 0.71125 0.000 0.928 0.004 0.056 0.000 0.012
#> GSM153144 2 0.3843 0.61304 0.000 0.740 0.232 0.016 0.004 0.008
#> GSM153145 5 0.1514 0.80617 0.000 0.004 0.036 0.004 0.944 0.012
#> GSM153146 2 0.1930 0.72446 0.000 0.924 0.012 0.000 0.028 0.036
#> GSM153147 3 0.3467 0.70557 0.000 0.084 0.832 0.008 0.008 0.068
#> GSM153148 2 0.1116 0.72433 0.000 0.960 0.004 0.008 0.000 0.028
#> GSM153149 2 0.3572 0.70779 0.000 0.836 0.060 0.008 0.028 0.068
#> GSM153150 6 0.4600 0.53411 0.008 0.144 0.000 0.132 0.000 0.716
#> GSM153151 6 0.4493 0.59211 0.000 0.120 0.112 0.016 0.004 0.748
#> GSM153152 2 0.5505 0.10066 0.000 0.492 0.424 0.008 0.016 0.060
#> GSM153153 2 0.2579 0.70341 0.000 0.876 0.032 0.004 0.088 0.000
#> GSM153154 5 0.4027 0.71158 0.000 0.064 0.156 0.012 0.768 0.000
#> GSM153155 2 0.3871 0.68265 0.000 0.796 0.124 0.064 0.008 0.008
#> GSM153156 3 0.3637 0.73840 0.000 0.028 0.832 0.012 0.084 0.044
#> GSM153157 5 0.4523 0.67114 0.000 0.000 0.044 0.196 0.724 0.036
#> GSM153158 5 0.2656 0.79771 0.000 0.044 0.060 0.004 0.884 0.008
#> GSM153159 5 0.2833 0.79331 0.000 0.004 0.088 0.008 0.868 0.032
#> GSM153160 3 0.2394 0.72979 0.000 0.000 0.900 0.020 0.048 0.032
#> GSM153161 2 0.3225 0.69209 0.000 0.828 0.008 0.024 0.004 0.136
#> GSM153162 3 0.2778 0.74580 0.004 0.048 0.884 0.012 0.048 0.004
#> GSM153163 3 0.4494 0.33869 0.000 0.016 0.572 0.012 0.400 0.000
#> GSM153164 5 0.3734 0.76475 0.000 0.068 0.040 0.064 0.824 0.004
#> GSM153165 3 0.3415 0.71832 0.000 0.028 0.808 0.012 0.152 0.000
#> GSM153166 2 0.5334 0.52740 0.000 0.652 0.208 0.020 0.116 0.004
#> GSM153167 3 0.4710 0.61798 0.000 0.216 0.708 0.036 0.032 0.008
#> GSM153168 5 0.2112 0.79946 0.000 0.000 0.036 0.020 0.916 0.028
#> GSM153169 3 0.3810 0.66890 0.000 0.008 0.748 0.008 0.224 0.012
#> GSM153170 3 0.3106 0.73800 0.000 0.040 0.844 0.004 0.108 0.004
#> GSM153171 3 0.7764 -0.11307 0.080 0.036 0.356 0.284 0.000 0.244
#> GSM153172 2 0.2145 0.71589 0.000 0.904 0.076 0.012 0.004 0.004
#> GSM153173 3 0.3514 0.67826 0.000 0.020 0.768 0.004 0.208 0.000
#> GSM153174 3 0.3589 0.64173 0.004 0.208 0.768 0.008 0.000 0.012
#> GSM153175 3 0.4755 0.55377 0.088 0.012 0.728 0.160 0.004 0.008
#> GSM153176 3 0.4591 0.59144 0.024 0.000 0.752 0.156 0.028 0.040
#> GSM153177 2 0.3994 0.68567 0.000 0.804 0.112 0.016 0.040 0.028
#> GSM152931 2 0.6482 0.01684 0.040 0.420 0.144 0.392 0.000 0.004
#> GSM152932 2 0.2975 0.71142 0.000 0.860 0.088 0.004 0.008 0.040
#> GSM152933 2 0.5155 0.53992 0.000 0.664 0.068 0.008 0.236 0.024
#> GSM152934 6 0.4543 0.62463 0.004 0.084 0.028 0.068 0.032 0.784
#> GSM152935 6 0.4966 0.58094 0.000 0.104 0.024 0.012 0.140 0.720
#> GSM152936 6 0.6972 0.02930 0.000 0.360 0.084 0.176 0.000 0.380
#> GSM152937 6 0.2976 0.62229 0.008 0.008 0.096 0.008 0.016 0.864
#> GSM152938 6 0.5102 -0.02105 0.004 0.016 0.472 0.012 0.016 0.480
#> GSM152939 3 0.4753 0.58814 0.048 0.064 0.744 0.136 0.000 0.008
#> GSM152940 6 0.5008 0.48826 0.004 0.112 0.008 0.204 0.000 0.672
#> GSM152941 4 0.5340 0.06319 0.048 0.012 0.004 0.548 0.008 0.380
#> GSM152942 3 0.1890 0.71931 0.000 0.000 0.924 0.044 0.024 0.008
#> GSM152943 6 0.3127 0.61605 0.000 0.100 0.004 0.056 0.000 0.840
#> GSM152944 5 0.4349 0.54751 0.000 0.048 0.264 0.004 0.684 0.000
#> GSM152945 6 0.2322 0.63020 0.008 0.040 0.012 0.004 0.024 0.912
#> GSM152946 2 0.7143 0.37019 0.004 0.488 0.204 0.116 0.004 0.184
#> GSM152947 6 0.3845 0.59094 0.024 0.008 0.056 0.100 0.000 0.812
#> GSM152948 2 0.1760 0.72309 0.004 0.936 0.012 0.028 0.000 0.020
#> GSM152949 3 0.2907 0.74554 0.000 0.056 0.868 0.004 0.064 0.008
#> GSM152950 3 0.7251 0.17965 0.000 0.328 0.400 0.016 0.072 0.184
#> GSM152951 2 0.1718 0.71710 0.000 0.932 0.008 0.044 0.000 0.016
#> GSM152952 2 0.2575 0.70864 0.000 0.880 0.000 0.044 0.004 0.072
#> GSM152953 2 0.3160 0.69986 0.000 0.836 0.020 0.012 0.004 0.128
#> GSM152954 4 0.5131 0.44074 0.028 0.132 0.020 0.740 0.024 0.056
#> GSM152955 5 0.6164 0.27839 0.000 0.008 0.008 0.232 0.508 0.244
#> GSM152956 2 0.1036 0.72456 0.000 0.964 0.008 0.004 0.000 0.024
#> GSM152957 4 0.6193 0.11399 0.104 0.000 0.408 0.448 0.008 0.032
#> GSM152958 2 0.6024 -0.01066 0.060 0.452 0.024 0.436 0.000 0.028
#> GSM152959 4 0.5455 0.31798 0.020 0.004 0.100 0.664 0.012 0.200
#> GSM152960 2 0.5605 0.19380 0.000 0.488 0.000 0.152 0.000 0.360
#> GSM152961 4 0.6448 0.32817 0.080 0.288 0.016 0.540 0.000 0.076
#> GSM152962 6 0.5063 0.54901 0.000 0.100 0.192 0.004 0.020 0.684
#> GSM152963 2 0.2865 0.69636 0.000 0.852 0.004 0.020 0.004 0.120
#> GSM152964 6 0.4645 0.51741 0.012 0.000 0.008 0.052 0.228 0.700
#> GSM152965 2 0.4667 0.26273 0.000 0.552 0.008 0.016 0.008 0.416
#> GSM152966 2 0.5961 0.05649 0.036 0.456 0.096 0.412 0.000 0.000
#> GSM152967 2 0.2699 0.71685 0.000 0.888 0.052 0.036 0.016 0.008
#> GSM152968 3 0.4912 0.67396 0.000 0.180 0.704 0.008 0.092 0.016
#> GSM152969 4 0.5498 0.22022 0.020 0.364 0.044 0.556 0.004 0.012
#> GSM152970 6 0.6279 0.09014 0.024 0.000 0.176 0.364 0.000 0.436
#> GSM152971 4 0.6153 -0.02289 0.044 0.424 0.080 0.444 0.000 0.008
#> GSM152972 2 0.5453 0.29228 0.004 0.556 0.020 0.352 0.000 0.068
#> GSM152973 3 0.2998 0.65665 0.064 0.000 0.856 0.072 0.000 0.008
#> GSM152974 2 0.3543 0.69929 0.000 0.816 0.120 0.008 0.004 0.052
#> GSM152975 2 0.5585 0.08354 0.000 0.456 0.028 0.068 0.448 0.000
#> GSM152976 4 0.6615 0.08852 0.148 0.016 0.392 0.420 0.008 0.016
#> GSM152977 4 0.4890 0.36114 0.016 0.008 0.032 0.716 0.200 0.028
#> GSM152978 4 0.4980 0.38014 0.004 0.296 0.000 0.632 0.016 0.052
#> GSM152979 3 0.3541 0.67867 0.000 0.004 0.772 0.004 0.204 0.016
#> GSM152980 4 0.5948 0.36403 0.000 0.280 0.044 0.592 0.056 0.028
#> GSM152981 5 0.3063 0.76464 0.000 0.000 0.024 0.064 0.860 0.052
#> GSM152982 3 0.6440 0.22232 0.004 0.048 0.508 0.352 0.040 0.048
#> GSM152983 4 0.6544 0.28199 0.020 0.292 0.124 0.528 0.008 0.028
#> GSM152984 3 0.2432 0.72433 0.004 0.020 0.908 0.036 0.024 0.008
#> GSM152985 4 0.5134 0.33858 0.040 0.012 0.012 0.724 0.056 0.156
#> GSM152986 2 0.6366 0.04139 0.120 0.452 0.044 0.380 0.000 0.004
#> GSM152987 6 0.2971 0.58297 0.032 0.012 0.004 0.080 0.004 0.868
#> GSM152988 3 0.3960 0.61662 0.100 0.012 0.792 0.092 0.004 0.000
#> GSM152989 4 0.5957 0.40436 0.204 0.008 0.080 0.624 0.000 0.084
#> GSM152990 3 0.2657 0.73779 0.000 0.012 0.888 0.008 0.060 0.032
#> GSM152991 5 0.6751 0.40540 0.000 0.172 0.044 0.040 0.556 0.188
#> GSM187524 6 0.5835 0.12029 0.064 0.000 0.004 0.420 0.040 0.472
#> GSM187525 4 0.5505 0.10213 0.064 0.000 0.004 0.584 0.032 0.316
#> GSM187526 4 0.6281 0.17804 0.248 0.000 0.004 0.516 0.024 0.208
#> GSM187527 1 0.1983 0.82569 0.908 0.000 0.020 0.072 0.000 0.000
#> GSM152856 1 0.0951 0.83033 0.968 0.008 0.000 0.020 0.000 0.004
#> GSM152857 1 0.1223 0.83121 0.960 0.000 0.008 0.012 0.016 0.004
#> GSM152858 1 0.5744 0.39770 0.520 0.000 0.016 0.372 0.012 0.080
#> GSM152859 6 0.6535 0.06071 0.132 0.000 0.012 0.400 0.036 0.420
#> GSM152860 4 0.6621 -0.08057 0.352 0.000 0.012 0.448 0.036 0.152
#> GSM152861 1 0.3734 0.74593 0.776 0.000 0.008 0.184 0.004 0.028
#> GSM152862 4 0.6378 -0.14352 0.380 0.000 0.012 0.460 0.036 0.112
#> GSM152863 1 0.2830 0.81992 0.868 0.000 0.024 0.092 0.004 0.012
#> GSM152864 1 0.2455 0.81399 0.872 0.000 0.000 0.112 0.004 0.012
#> GSM152865 1 0.3751 0.76065 0.784 0.000 0.020 0.172 0.004 0.020
#> GSM152866 1 0.5262 0.51222 0.600 0.004 0.004 0.084 0.004 0.304
#> GSM152867 1 0.1699 0.82947 0.928 0.000 0.004 0.060 0.004 0.004
#> GSM152868 1 0.2306 0.81995 0.888 0.000 0.004 0.096 0.004 0.008
#> GSM152869 1 0.2451 0.81979 0.876 0.000 0.004 0.108 0.004 0.008
#> GSM152870 4 0.6441 0.00556 0.316 0.000 0.012 0.496 0.032 0.144
#> GSM152871 1 0.4892 0.54730 0.604 0.000 0.016 0.344 0.008 0.028
#> GSM152872 1 0.6092 0.27662 0.464 0.000 0.016 0.408 0.024 0.088
#> GSM152873 1 0.1536 0.82855 0.944 0.000 0.012 0.024 0.000 0.020
#> GSM152874 1 0.3103 0.78973 0.848 0.000 0.016 0.036 0.000 0.100
#> GSM152875 1 0.2411 0.81800 0.900 0.000 0.024 0.032 0.000 0.044
#> GSM152876 1 0.1921 0.81049 0.928 0.004 0.024 0.032 0.000 0.012
#> GSM152877 1 0.1930 0.82453 0.924 0.000 0.012 0.028 0.000 0.036
#> GSM152878 1 0.1871 0.81747 0.928 0.000 0.016 0.032 0.000 0.024
#> GSM152879 1 0.0622 0.83400 0.980 0.000 0.000 0.008 0.000 0.012
#> GSM152880 1 0.0837 0.83516 0.972 0.000 0.004 0.020 0.000 0.004
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> CV:NMF 167 3.11e-15 2
#> CV:NMF 137 4.98e-14 3
#> CV:NMF 108 1.85e-16 4
#> CV:NMF 136 5.81e-26 5
#> CV:NMF 116 1.16e-23 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "hclust"]
# you can also extract it by
# res = res_list["MAD:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.409 0.697 0.860 0.3993 0.574 0.574
#> 3 3 0.339 0.603 0.768 0.2861 0.946 0.906
#> 4 4 0.388 0.542 0.725 0.1513 0.815 0.666
#> 5 5 0.406 0.393 0.678 0.0846 0.683 0.430
#> 6 6 0.414 0.359 0.673 0.0380 0.940 0.854
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.6343 0.81084 0.160 0.840
#> GSM152805 2 0.0000 0.84573 0.000 1.000
#> GSM152806 2 0.0000 0.84573 0.000 1.000
#> GSM152807 2 0.7056 0.78504 0.192 0.808
#> GSM152808 2 0.0000 0.84573 0.000 1.000
#> GSM152809 2 0.7056 0.78504 0.192 0.808
#> GSM152810 2 0.9944 0.07748 0.456 0.544
#> GSM152811 2 0.8861 0.52726 0.304 0.696
#> GSM152812 2 0.6887 0.79254 0.184 0.816
#> GSM152813 2 0.4939 0.84429 0.108 0.892
#> GSM152814 2 0.6712 0.79982 0.176 0.824
#> GSM152815 2 0.7299 0.77496 0.204 0.796
#> GSM152816 2 0.2236 0.85733 0.036 0.964
#> GSM152817 2 0.0000 0.84573 0.000 1.000
#> GSM152818 2 0.0000 0.84573 0.000 1.000
#> GSM152819 2 0.2948 0.85787 0.052 0.948
#> GSM152820 2 0.8081 0.70398 0.248 0.752
#> GSM152821 2 0.5842 0.82517 0.140 0.860
#> GSM153115 2 1.0000 -0.06282 0.500 0.500
#> GSM153116 2 0.0376 0.84767 0.004 0.996
#> GSM153117 2 0.2423 0.85796 0.040 0.960
#> GSM153118 2 0.5519 0.83186 0.128 0.872
#> GSM153119 2 0.0000 0.84573 0.000 1.000
#> GSM153120 1 0.9635 0.38885 0.612 0.388
#> GSM153121 2 0.0672 0.84933 0.008 0.992
#> GSM153122 2 0.0000 0.84573 0.000 1.000
#> GSM153123 2 0.2236 0.85805 0.036 0.964
#> GSM153124 2 0.8909 0.58105 0.308 0.692
#> GSM153125 1 0.9998 0.07938 0.508 0.492
#> GSM153126 2 0.0376 0.84765 0.004 0.996
#> GSM153127 2 0.7528 0.76063 0.216 0.784
#> GSM153128 2 0.0938 0.85135 0.012 0.988
#> GSM153129 2 0.3879 0.85367 0.076 0.924
#> GSM153130 2 0.0000 0.84573 0.000 1.000
#> GSM153131 2 0.2423 0.85779 0.040 0.960
#> GSM153132 2 0.2043 0.85596 0.032 0.968
#> GSM153133 2 0.2778 0.85749 0.048 0.952
#> GSM153134 2 0.3584 0.85509 0.068 0.932
#> GSM153135 2 0.7453 0.76526 0.212 0.788
#> GSM153136 1 0.9896 0.26828 0.560 0.440
#> GSM153137 2 0.8555 0.66623 0.280 0.720
#> GSM153138 2 0.6973 0.78830 0.188 0.812
#> GSM153139 2 0.0000 0.84573 0.000 1.000
#> GSM153140 2 0.4431 0.84986 0.092 0.908
#> GSM153141 2 0.7453 0.76525 0.212 0.788
#> GSM153142 2 0.0000 0.84573 0.000 1.000
#> GSM153143 2 0.6623 0.80471 0.172 0.828
#> GSM153144 2 0.2603 0.85729 0.044 0.956
#> GSM153145 2 0.0000 0.84573 0.000 1.000
#> GSM153146 2 0.5946 0.82288 0.144 0.856
#> GSM153147 2 0.1414 0.85287 0.020 0.980
#> GSM153148 2 0.7453 0.76496 0.212 0.788
#> GSM153149 2 0.3733 0.85454 0.072 0.928
#> GSM153150 1 0.9661 0.37974 0.608 0.392
#> GSM153151 2 0.1843 0.85626 0.028 0.972
#> GSM153152 2 0.2236 0.85639 0.036 0.964
#> GSM153153 2 0.4161 0.85243 0.084 0.916
#> GSM153154 2 0.2043 0.85619 0.032 0.968
#> GSM153155 2 0.5408 0.83539 0.124 0.876
#> GSM153156 2 0.0376 0.84787 0.004 0.996
#> GSM153157 2 0.0672 0.84955 0.008 0.992
#> GSM153158 2 0.1633 0.85497 0.024 0.976
#> GSM153159 2 0.0000 0.84573 0.000 1.000
#> GSM153160 2 0.0000 0.84573 0.000 1.000
#> GSM153161 2 0.7950 0.72914 0.240 0.760
#> GSM153162 2 0.2603 0.85764 0.044 0.956
#> GSM153163 2 0.0000 0.84573 0.000 1.000
#> GSM153164 2 0.4939 0.84473 0.108 0.892
#> GSM153165 2 0.0000 0.84573 0.000 1.000
#> GSM153166 2 0.4431 0.84986 0.092 0.908
#> GSM153167 2 0.3431 0.85579 0.064 0.936
#> GSM153168 2 0.0000 0.84573 0.000 1.000
#> GSM153169 2 0.0376 0.84787 0.004 0.996
#> GSM153170 2 0.0376 0.84805 0.004 0.996
#> GSM153171 2 0.9896 0.22008 0.440 0.560
#> GSM153172 2 0.5059 0.84185 0.112 0.888
#> GSM153173 2 0.0000 0.84573 0.000 1.000
#> GSM153174 2 0.2778 0.85758 0.048 0.952
#> GSM153175 2 0.9963 0.07763 0.464 0.536
#> GSM153176 2 0.9754 0.29283 0.408 0.592
#> GSM153177 2 0.3431 0.85661 0.064 0.936
#> GSM152931 1 0.9993 0.11598 0.516 0.484
#> GSM152932 2 0.4815 0.84522 0.104 0.896
#> GSM152933 2 0.5519 0.83207 0.128 0.872
#> GSM152934 2 0.7674 0.74010 0.224 0.776
#> GSM152935 2 0.2236 0.85595 0.036 0.964
#> GSM152936 2 0.9909 0.19692 0.444 0.556
#> GSM152937 2 0.0672 0.84925 0.008 0.992
#> GSM152938 2 0.0672 0.84925 0.008 0.992
#> GSM152939 2 0.5178 0.83157 0.116 0.884
#> GSM152940 1 0.8713 0.54280 0.708 0.292
#> GSM152941 1 0.1843 0.75673 0.972 0.028
#> GSM152942 2 0.2778 0.85678 0.048 0.952
#> GSM152943 2 0.7815 0.73678 0.232 0.768
#> GSM152944 2 0.0000 0.84573 0.000 1.000
#> GSM152945 2 0.1184 0.84567 0.016 0.984
#> GSM152946 2 0.6887 0.78272 0.184 0.816
#> GSM152947 1 0.9635 0.38822 0.612 0.388
#> GSM152948 2 0.6801 0.79743 0.180 0.820
#> GSM152949 2 0.2423 0.85704 0.040 0.960
#> GSM152950 2 0.2603 0.85807 0.044 0.956
#> GSM152951 2 0.6712 0.80014 0.176 0.824
#> GSM152952 2 0.7674 0.75132 0.224 0.776
#> GSM152953 2 0.6712 0.79967 0.176 0.824
#> GSM152954 2 0.9933 0.17370 0.452 0.548
#> GSM152955 2 0.6973 0.78593 0.188 0.812
#> GSM152956 2 0.7528 0.76062 0.216 0.784
#> GSM152957 1 0.9970 0.17803 0.532 0.468
#> GSM152958 1 0.9896 0.26794 0.560 0.440
#> GSM152959 1 0.9881 0.27638 0.564 0.436
#> GSM152960 1 0.9944 0.21472 0.544 0.456
#> GSM152961 1 0.8955 0.51510 0.688 0.312
#> GSM152962 2 0.1414 0.85363 0.020 0.980
#> GSM152963 2 0.7453 0.76390 0.212 0.788
#> GSM152964 2 0.0376 0.84792 0.004 0.996
#> GSM152965 2 0.4431 0.85186 0.092 0.908
#> GSM152966 1 0.9988 0.14014 0.520 0.480
#> GSM152967 2 0.3114 0.85758 0.056 0.944
#> GSM152968 2 0.2043 0.85588 0.032 0.968
#> GSM152969 1 0.9983 0.14704 0.524 0.476
#> GSM152970 1 0.9922 0.23500 0.552 0.448
#> GSM152971 1 0.9977 0.16248 0.528 0.472
#> GSM152972 1 0.9909 0.25648 0.556 0.444
#> GSM152973 2 0.4431 0.84438 0.092 0.908
#> GSM152974 2 0.4298 0.85189 0.088 0.912
#> GSM152975 2 0.9170 0.52936 0.332 0.668
#> GSM152976 2 0.9996 -0.00664 0.488 0.512
#> GSM152977 2 0.9988 0.03203 0.480 0.520
#> GSM152978 2 0.9922 0.18946 0.448 0.552
#> GSM152979 2 0.0000 0.84573 0.000 1.000
#> GSM152980 2 0.8144 0.69699 0.252 0.748
#> GSM152981 2 0.0000 0.84573 0.000 1.000
#> GSM152982 2 0.9996 -0.00866 0.488 0.512
#> GSM152983 1 0.9993 0.11190 0.516 0.484
#> GSM152984 2 0.4939 0.83708 0.108 0.892
#> GSM152985 1 0.8813 0.53088 0.700 0.300
#> GSM152986 1 0.9922 0.24417 0.552 0.448
#> GSM152987 1 0.3274 0.74009 0.940 0.060
#> GSM152988 2 0.3879 0.85076 0.076 0.924
#> GSM152989 1 0.9944 0.21219 0.544 0.456
#> GSM152990 2 0.0376 0.84805 0.004 0.996
#> GSM152991 2 0.2423 0.85794 0.040 0.960
#> GSM187524 1 0.0376 0.76514 0.996 0.004
#> GSM187525 1 0.0376 0.76514 0.996 0.004
#> GSM187526 1 0.0376 0.76514 0.996 0.004
#> GSM187527 1 0.1184 0.76134 0.984 0.016
#> GSM152856 1 0.0376 0.76514 0.996 0.004
#> GSM152857 1 0.1184 0.76134 0.984 0.016
#> GSM152858 1 0.0376 0.76514 0.996 0.004
#> GSM152859 1 0.3584 0.73785 0.932 0.068
#> GSM152860 1 0.0376 0.76514 0.996 0.004
#> GSM152861 1 0.0376 0.76514 0.996 0.004
#> GSM152862 1 0.0376 0.76514 0.996 0.004
#> GSM152863 1 0.0376 0.76514 0.996 0.004
#> GSM152864 1 0.0376 0.76514 0.996 0.004
#> GSM152865 1 0.0376 0.76514 0.996 0.004
#> GSM152866 1 0.0376 0.76514 0.996 0.004
#> GSM152867 1 0.0376 0.76514 0.996 0.004
#> GSM152868 1 0.0376 0.76514 0.996 0.004
#> GSM152869 1 0.0376 0.76514 0.996 0.004
#> GSM152870 1 0.0376 0.76514 0.996 0.004
#> GSM152871 1 0.0376 0.76514 0.996 0.004
#> GSM152872 1 0.0376 0.76514 0.996 0.004
#> GSM152873 1 0.0376 0.76514 0.996 0.004
#> GSM152874 1 0.0376 0.76514 0.996 0.004
#> GSM152875 1 0.0376 0.76514 0.996 0.004
#> GSM152876 1 0.1184 0.76134 0.984 0.016
#> GSM152877 1 0.0376 0.76514 0.996 0.004
#> GSM152878 1 0.0376 0.76514 0.996 0.004
#> GSM152879 1 0.0376 0.76514 0.996 0.004
#> GSM152880 1 0.0376 0.76514 0.996 0.004
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 3 0.5737 0.5331 0.012 0.256 0.732
#> GSM152805 3 0.4399 0.5881 0.000 0.188 0.812
#> GSM152806 3 0.4399 0.5881 0.000 0.188 0.812
#> GSM152807 3 0.6113 0.4626 0.012 0.300 0.688
#> GSM152808 3 0.4399 0.5881 0.000 0.188 0.812
#> GSM152809 3 0.6113 0.4626 0.012 0.300 0.688
#> GSM152810 2 0.7777 0.0568 0.060 0.576 0.364
#> GSM152811 3 0.6819 0.1626 0.012 0.476 0.512
#> GSM152812 3 0.6019 0.4820 0.012 0.288 0.700
#> GSM152813 3 0.4645 0.6376 0.008 0.176 0.816
#> GSM152814 3 0.5623 0.5122 0.004 0.280 0.716
#> GSM152815 3 0.6172 0.4476 0.012 0.308 0.680
#> GSM152816 3 0.2959 0.6997 0.000 0.100 0.900
#> GSM152817 3 0.4399 0.5881 0.000 0.188 0.812
#> GSM152818 3 0.4399 0.5881 0.000 0.188 0.812
#> GSM152819 3 0.3879 0.6881 0.000 0.152 0.848
#> GSM152820 3 0.7267 0.3610 0.064 0.268 0.668
#> GSM152821 3 0.4796 0.5972 0.000 0.220 0.780
#> GSM153115 3 0.9717 -0.7737 0.220 0.384 0.396
#> GSM153116 3 0.3879 0.6423 0.000 0.152 0.848
#> GSM153117 3 0.2959 0.7028 0.000 0.100 0.900
#> GSM153118 3 0.4733 0.6169 0.004 0.196 0.800
#> GSM153119 3 0.3192 0.6537 0.000 0.112 0.888
#> GSM153120 2 0.9759 0.7644 0.284 0.444 0.272
#> GSM153121 3 0.2356 0.6766 0.000 0.072 0.928
#> GSM153122 3 0.3551 0.6471 0.000 0.132 0.868
#> GSM153123 3 0.2878 0.7040 0.000 0.096 0.904
#> GSM153124 3 0.8233 0.0704 0.116 0.272 0.612
#> GSM153125 2 0.9651 0.7746 0.208 0.400 0.392
#> GSM153126 3 0.2537 0.6733 0.000 0.080 0.920
#> GSM153127 3 0.6501 0.4129 0.020 0.316 0.664
#> GSM153128 3 0.2796 0.6800 0.000 0.092 0.908
#> GSM153129 3 0.3349 0.6871 0.004 0.108 0.888
#> GSM153130 3 0.2711 0.6684 0.000 0.088 0.912
#> GSM153131 3 0.2878 0.7025 0.000 0.096 0.904
#> GSM153132 3 0.2356 0.7015 0.000 0.072 0.928
#> GSM153133 3 0.2537 0.6981 0.000 0.080 0.920
#> GSM153134 3 0.3340 0.6865 0.000 0.120 0.880
#> GSM153135 3 0.6369 0.4221 0.016 0.316 0.668
#> GSM153136 2 0.9830 0.8324 0.252 0.408 0.340
#> GSM153137 3 0.7263 0.1766 0.036 0.372 0.592
#> GSM153138 3 0.6062 0.4922 0.016 0.276 0.708
#> GSM153139 3 0.2625 0.6702 0.000 0.084 0.916
#> GSM153140 3 0.4209 0.6716 0.016 0.128 0.856
#> GSM153141 3 0.6341 0.4277 0.016 0.312 0.672
#> GSM153142 3 0.3482 0.6372 0.000 0.128 0.872
#> GSM153143 3 0.5858 0.5476 0.020 0.240 0.740
#> GSM153144 3 0.2400 0.6994 0.004 0.064 0.932
#> GSM153145 3 0.4399 0.5881 0.000 0.188 0.812
#> GSM153146 3 0.4796 0.5977 0.000 0.220 0.780
#> GSM153147 3 0.1643 0.6963 0.000 0.044 0.956
#> GSM153148 3 0.6228 0.4326 0.012 0.316 0.672
#> GSM153149 3 0.3686 0.6790 0.000 0.140 0.860
#> GSM153150 2 0.9757 0.7995 0.268 0.444 0.288
#> GSM153151 3 0.1753 0.7022 0.000 0.048 0.952
#> GSM153152 3 0.1964 0.6998 0.000 0.056 0.944
#> GSM153153 3 0.4172 0.6568 0.004 0.156 0.840
#> GSM153154 3 0.2261 0.7020 0.000 0.068 0.932
#> GSM153155 3 0.4784 0.6150 0.004 0.200 0.796
#> GSM153156 3 0.2066 0.6810 0.000 0.060 0.940
#> GSM153157 3 0.3192 0.6593 0.000 0.112 0.888
#> GSM153158 3 0.2448 0.6984 0.000 0.076 0.924
#> GSM153159 3 0.2711 0.6652 0.000 0.088 0.912
#> GSM153160 3 0.2625 0.6707 0.000 0.084 0.916
#> GSM153161 3 0.6627 0.3600 0.020 0.336 0.644
#> GSM153162 3 0.2301 0.6995 0.004 0.060 0.936
#> GSM153163 3 0.2625 0.6702 0.000 0.084 0.916
#> GSM153164 3 0.4602 0.6591 0.016 0.152 0.832
#> GSM153165 3 0.2537 0.6723 0.000 0.080 0.920
#> GSM153166 3 0.4099 0.6648 0.008 0.140 0.852
#> GSM153167 3 0.3267 0.6883 0.000 0.116 0.884
#> GSM153168 3 0.4399 0.5881 0.000 0.188 0.812
#> GSM153169 3 0.2711 0.6770 0.000 0.088 0.912
#> GSM153170 3 0.2625 0.6793 0.000 0.084 0.916
#> GSM153171 3 0.9319 -0.5511 0.168 0.368 0.464
#> GSM153172 3 0.4629 0.6319 0.004 0.188 0.808
#> GSM153173 3 0.2537 0.6723 0.000 0.080 0.920
#> GSM153174 3 0.2301 0.6987 0.004 0.060 0.936
#> GSM153175 3 0.9570 -0.6614 0.204 0.348 0.448
#> GSM153176 3 0.9239 -0.4840 0.172 0.328 0.500
#> GSM153177 3 0.2682 0.6984 0.004 0.076 0.920
#> GSM152931 2 0.9737 0.7946 0.224 0.392 0.384
#> GSM152932 3 0.4351 0.6529 0.004 0.168 0.828
#> GSM152933 3 0.4555 0.6174 0.000 0.200 0.800
#> GSM152934 3 0.7022 0.4580 0.068 0.232 0.700
#> GSM152935 3 0.3412 0.7005 0.000 0.124 0.876
#> GSM152936 3 0.9335 -0.5811 0.168 0.376 0.456
#> GSM152937 3 0.2356 0.6829 0.000 0.072 0.928
#> GSM152938 3 0.2448 0.6825 0.000 0.076 0.924
#> GSM152939 3 0.4712 0.6507 0.044 0.108 0.848
#> GSM152940 2 0.9479 0.6673 0.348 0.460 0.192
#> GSM152941 1 0.6016 0.5897 0.724 0.256 0.020
#> GSM152942 3 0.3207 0.7017 0.012 0.084 0.904
#> GSM152943 3 0.6906 0.3401 0.032 0.324 0.644
#> GSM152944 3 0.2625 0.6702 0.000 0.084 0.916
#> GSM152945 3 0.4178 0.6658 0.000 0.172 0.828
#> GSM152946 3 0.6054 0.5622 0.052 0.180 0.768
#> GSM152947 2 0.9838 0.7932 0.288 0.424 0.288
#> GSM152948 3 0.6187 0.5198 0.028 0.248 0.724
#> GSM152949 3 0.2200 0.6984 0.004 0.056 0.940
#> GSM152950 3 0.2590 0.7019 0.004 0.072 0.924
#> GSM152951 3 0.5986 0.5433 0.024 0.240 0.736
#> GSM152952 3 0.6553 0.3938 0.020 0.324 0.656
#> GSM152953 3 0.6053 0.5112 0.020 0.260 0.720
#> GSM152954 3 0.9527 -0.6241 0.192 0.372 0.436
#> GSM152955 3 0.6556 0.4689 0.032 0.276 0.692
#> GSM152956 3 0.6282 0.4142 0.012 0.324 0.664
#> GSM152957 2 0.9678 0.8114 0.216 0.420 0.364
#> GSM152958 2 0.9823 0.8320 0.252 0.412 0.336
#> GSM152959 2 0.9787 0.8259 0.248 0.424 0.328
#> GSM152960 2 0.9760 0.8165 0.236 0.420 0.344
#> GSM152961 2 0.9596 0.7268 0.336 0.452 0.212
#> GSM152962 3 0.2066 0.6995 0.000 0.060 0.940
#> GSM152963 3 0.6369 0.4183 0.016 0.316 0.668
#> GSM152964 3 0.4291 0.6397 0.000 0.180 0.820
#> GSM152965 3 0.3784 0.6814 0.004 0.132 0.864
#> GSM152966 2 0.9693 0.8023 0.216 0.404 0.380
#> GSM152967 3 0.3349 0.6962 0.004 0.108 0.888
#> GSM152968 3 0.1753 0.6977 0.000 0.048 0.952
#> GSM152969 2 0.9690 0.8033 0.216 0.408 0.376
#> GSM152970 2 0.9797 0.8127 0.240 0.404 0.356
#> GSM152971 2 0.9732 0.8075 0.224 0.404 0.372
#> GSM152972 2 0.9812 0.8319 0.248 0.412 0.340
#> GSM152973 3 0.3973 0.6791 0.032 0.088 0.880
#> GSM152974 3 0.4110 0.6743 0.004 0.152 0.844
#> GSM152975 3 0.8362 -0.0305 0.112 0.300 0.588
#> GSM152976 3 0.9576 -0.7333 0.196 0.396 0.408
#> GSM152977 3 0.9569 -0.7046 0.196 0.384 0.420
#> GSM152978 3 0.9496 -0.6073 0.188 0.372 0.440
#> GSM152979 3 0.2448 0.6832 0.000 0.076 0.924
#> GSM152980 3 0.7351 0.3508 0.068 0.268 0.664
#> GSM152981 3 0.4399 0.5881 0.000 0.188 0.812
#> GSM152982 3 0.9593 -0.7195 0.200 0.380 0.420
#> GSM152983 2 0.9736 0.7959 0.224 0.396 0.380
#> GSM152984 3 0.4479 0.6591 0.044 0.096 0.860
#> GSM152985 2 0.9541 0.7031 0.348 0.452 0.200
#> GSM152986 2 0.9800 0.8304 0.244 0.412 0.344
#> GSM152987 1 0.5115 0.7570 0.796 0.188 0.016
#> GSM152988 3 0.3415 0.6902 0.020 0.080 0.900
#> GSM152989 2 0.9714 0.8200 0.224 0.420 0.356
#> GSM152990 3 0.2711 0.6821 0.000 0.088 0.912
#> GSM152991 3 0.2356 0.7036 0.000 0.072 0.928
#> GSM187524 1 0.0747 0.9544 0.984 0.016 0.000
#> GSM187525 1 0.0747 0.9544 0.984 0.016 0.000
#> GSM187526 1 0.0592 0.9551 0.988 0.012 0.000
#> GSM187527 1 0.1337 0.9449 0.972 0.016 0.012
#> GSM152856 1 0.0747 0.9548 0.984 0.016 0.000
#> GSM152857 1 0.1337 0.9449 0.972 0.016 0.012
#> GSM152858 1 0.0747 0.9544 0.984 0.016 0.000
#> GSM152859 1 0.7460 0.5105 0.524 0.440 0.036
#> GSM152860 1 0.0747 0.9544 0.984 0.016 0.000
#> GSM152861 1 0.0592 0.9551 0.988 0.012 0.000
#> GSM152862 1 0.0747 0.9544 0.984 0.016 0.000
#> GSM152863 1 0.0000 0.9568 1.000 0.000 0.000
#> GSM152864 1 0.0000 0.9568 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.9568 1.000 0.000 0.000
#> GSM152866 1 0.0592 0.9555 0.988 0.012 0.000
#> GSM152867 1 0.0000 0.9568 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.9568 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.9568 1.000 0.000 0.000
#> GSM152870 1 0.0747 0.9544 0.984 0.016 0.000
#> GSM152871 1 0.0747 0.9544 0.984 0.016 0.000
#> GSM152872 1 0.0747 0.9544 0.984 0.016 0.000
#> GSM152873 1 0.0747 0.9548 0.984 0.016 0.000
#> GSM152874 1 0.0747 0.9548 0.984 0.016 0.000
#> GSM152875 1 0.0747 0.9548 0.984 0.016 0.000
#> GSM152876 1 0.1337 0.9449 0.972 0.016 0.012
#> GSM152877 1 0.0747 0.9548 0.984 0.016 0.000
#> GSM152878 1 0.0747 0.9548 0.984 0.016 0.000
#> GSM152879 1 0.0747 0.9548 0.984 0.016 0.000
#> GSM152880 1 0.0747 0.9548 0.984 0.016 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.5716 0.05481 0.000 0.552 0.028 0.420
#> GSM152805 2 0.4661 0.00830 0.000 0.652 0.348 0.000
#> GSM152806 2 0.4661 0.00830 0.000 0.652 0.348 0.000
#> GSM152807 2 0.5931 -0.14025 0.000 0.504 0.036 0.460
#> GSM152808 2 0.4661 0.00830 0.000 0.652 0.348 0.000
#> GSM152809 2 0.5931 -0.14025 0.000 0.504 0.036 0.460
#> GSM152810 3 0.5906 0.76996 0.032 0.180 0.728 0.060
#> GSM152811 3 0.5911 0.75871 0.004 0.328 0.624 0.044
#> GSM152812 2 0.5846 -0.08413 0.000 0.516 0.032 0.452
#> GSM152813 2 0.5152 0.41757 0.000 0.664 0.020 0.316
#> GSM152814 2 0.5815 0.02435 0.000 0.540 0.032 0.428
#> GSM152815 2 0.5861 -0.19489 0.000 0.488 0.032 0.480
#> GSM152816 2 0.4549 0.62699 0.000 0.804 0.096 0.100
#> GSM152817 2 0.4661 0.00830 0.000 0.652 0.348 0.000
#> GSM152818 2 0.4661 0.00830 0.000 0.652 0.348 0.000
#> GSM152819 2 0.5531 0.59295 0.000 0.732 0.140 0.128
#> GSM152820 2 0.5763 -0.17673 0.004 0.516 0.020 0.460
#> GSM152821 2 0.5496 0.25398 0.000 0.604 0.024 0.372
#> GSM153115 4 0.5187 0.74628 0.040 0.228 0.004 0.728
#> GSM153116 2 0.5235 0.38469 0.000 0.716 0.236 0.048
#> GSM153117 2 0.4875 0.63052 0.000 0.772 0.068 0.160
#> GSM153118 2 0.5355 0.30996 0.000 0.620 0.020 0.360
#> GSM153119 2 0.4086 0.37072 0.000 0.776 0.216 0.008
#> GSM153120 4 0.4821 0.64300 0.052 0.104 0.032 0.812
#> GSM153121 2 0.1388 0.63368 0.000 0.960 0.028 0.012
#> GSM153122 2 0.4576 0.24169 0.000 0.728 0.260 0.012
#> GSM153123 2 0.3577 0.62565 0.000 0.832 0.012 0.156
#> GSM153124 4 0.5421 0.40497 0.008 0.440 0.004 0.548
#> GSM153125 4 0.4888 0.74802 0.036 0.224 0.000 0.740
#> GSM153126 2 0.1452 0.61527 0.000 0.956 0.036 0.008
#> GSM153127 4 0.5937 0.23092 0.000 0.472 0.036 0.492
#> GSM153128 2 0.2443 0.62884 0.000 0.916 0.060 0.024
#> GSM153129 2 0.4123 0.58007 0.000 0.772 0.008 0.220
#> GSM153130 2 0.1824 0.58869 0.000 0.936 0.060 0.004
#> GSM153131 2 0.3991 0.62385 0.000 0.808 0.020 0.172
#> GSM153132 2 0.3734 0.65020 0.000 0.848 0.044 0.108
#> GSM153133 2 0.3933 0.59964 0.000 0.792 0.008 0.200
#> GSM153134 2 0.4053 0.56661 0.000 0.768 0.004 0.228
#> GSM153135 4 0.5938 0.21669 0.000 0.476 0.036 0.488
#> GSM153136 4 0.4830 0.73650 0.044 0.168 0.008 0.780
#> GSM153137 4 0.6076 0.43277 0.004 0.396 0.040 0.560
#> GSM153138 2 0.5760 -0.08536 0.000 0.524 0.028 0.448
#> GSM153139 2 0.2048 0.59269 0.000 0.928 0.064 0.008
#> GSM153140 2 0.4343 0.52181 0.000 0.732 0.004 0.264
#> GSM153141 4 0.5861 0.20491 0.000 0.480 0.032 0.488
#> GSM153142 2 0.4054 0.42304 0.000 0.796 0.188 0.016
#> GSM153143 2 0.6009 0.09785 0.004 0.560 0.036 0.400
#> GSM153144 2 0.3450 0.63116 0.000 0.836 0.008 0.156
#> GSM153145 2 0.4661 0.00830 0.000 0.652 0.348 0.000
#> GSM153146 2 0.5510 0.25118 0.000 0.600 0.024 0.376
#> GSM153147 2 0.2988 0.64452 0.000 0.876 0.012 0.112
#> GSM153148 4 0.5938 0.19747 0.000 0.480 0.036 0.484
#> GSM153149 2 0.4807 0.53889 0.000 0.728 0.024 0.248
#> GSM153150 4 0.4443 0.68573 0.048 0.120 0.012 0.820
#> GSM153151 2 0.2976 0.64669 0.000 0.872 0.008 0.120
#> GSM153152 2 0.3377 0.63619 0.000 0.848 0.012 0.140
#> GSM153153 2 0.5113 0.46925 0.000 0.684 0.024 0.292
#> GSM153154 2 0.3821 0.64747 0.000 0.840 0.040 0.120
#> GSM153155 2 0.5428 0.30740 0.004 0.620 0.016 0.360
#> GSM153156 2 0.1406 0.63790 0.000 0.960 0.024 0.016
#> GSM153157 2 0.3718 0.45879 0.000 0.820 0.168 0.012
#> GSM153158 2 0.4669 0.64005 0.000 0.796 0.100 0.104
#> GSM153159 2 0.2530 0.53521 0.000 0.888 0.112 0.000
#> GSM153160 2 0.1305 0.61029 0.000 0.960 0.036 0.004
#> GSM153161 4 0.5846 0.29408 0.000 0.452 0.032 0.516
#> GSM153162 2 0.3208 0.63227 0.000 0.848 0.004 0.148
#> GSM153163 2 0.1902 0.58774 0.000 0.932 0.064 0.004
#> GSM153164 2 0.5404 0.53281 0.000 0.700 0.052 0.248
#> GSM153165 2 0.1661 0.59982 0.000 0.944 0.052 0.004
#> GSM153166 2 0.4718 0.50338 0.000 0.708 0.012 0.280
#> GSM153167 2 0.4018 0.57158 0.000 0.772 0.004 0.224
#> GSM153168 2 0.4661 0.00830 0.000 0.652 0.348 0.000
#> GSM153169 2 0.2255 0.59805 0.000 0.920 0.068 0.012
#> GSM153170 2 0.2089 0.62241 0.000 0.932 0.048 0.020
#> GSM153171 4 0.5521 0.68103 0.032 0.300 0.004 0.664
#> GSM153172 2 0.5213 0.40108 0.000 0.652 0.020 0.328
#> GSM153173 2 0.1661 0.59982 0.000 0.944 0.052 0.004
#> GSM153174 2 0.3355 0.62726 0.000 0.836 0.004 0.160
#> GSM153175 4 0.5536 0.70812 0.032 0.280 0.008 0.680
#> GSM153176 4 0.5733 0.63477 0.028 0.332 0.008 0.632
#> GSM153177 2 0.4874 0.61747 0.000 0.764 0.056 0.180
#> GSM152931 4 0.4781 0.74944 0.036 0.212 0.000 0.752
#> GSM152932 2 0.5161 0.43982 0.000 0.676 0.024 0.300
#> GSM152933 2 0.5355 0.31022 0.000 0.620 0.020 0.360
#> GSM152934 2 0.5938 0.03372 0.008 0.544 0.024 0.424
#> GSM152935 2 0.4405 0.62018 0.000 0.800 0.048 0.152
#> GSM152936 4 0.5328 0.68760 0.020 0.292 0.008 0.680
#> GSM152937 2 0.1733 0.64376 0.000 0.948 0.028 0.024
#> GSM152938 2 0.1837 0.64443 0.000 0.944 0.028 0.028
#> GSM152939 2 0.4452 0.51777 0.000 0.732 0.008 0.260
#> GSM152940 4 0.4361 0.52877 0.092 0.048 0.024 0.836
#> GSM152941 1 0.5286 0.39918 0.604 0.004 0.008 0.384
#> GSM152942 2 0.3280 0.64732 0.000 0.860 0.016 0.124
#> GSM152943 4 0.6171 0.30428 0.004 0.456 0.040 0.500
#> GSM152944 2 0.2376 0.60309 0.000 0.916 0.068 0.016
#> GSM152945 2 0.6407 0.40741 0.000 0.648 0.204 0.148
#> GSM152946 2 0.5152 0.24660 0.004 0.608 0.004 0.384
#> GSM152947 4 0.4712 0.68458 0.060 0.132 0.008 0.800
#> GSM152948 2 0.5738 0.02694 0.000 0.540 0.028 0.432
#> GSM152949 2 0.3217 0.63994 0.000 0.860 0.012 0.128
#> GSM152950 2 0.3266 0.65053 0.000 0.868 0.024 0.108
#> GSM152951 2 0.5691 0.09087 0.000 0.564 0.028 0.408
#> GSM152952 4 0.5933 0.25276 0.000 0.464 0.036 0.500
#> GSM152953 2 0.5668 -0.04100 0.000 0.532 0.024 0.444
#> GSM152954 4 0.5551 0.70945 0.032 0.264 0.012 0.692
#> GSM152955 2 0.6031 0.00493 0.000 0.536 0.044 0.420
#> GSM152956 4 0.5937 0.22470 0.000 0.472 0.036 0.492
#> GSM152957 4 0.4669 0.74895 0.036 0.200 0.000 0.764
#> GSM152958 4 0.4770 0.73543 0.048 0.168 0.004 0.780
#> GSM152959 4 0.4946 0.72973 0.052 0.164 0.008 0.776
#> GSM152960 4 0.5347 0.73355 0.048 0.176 0.020 0.756
#> GSM152961 4 0.3896 0.59746 0.068 0.056 0.016 0.860
#> GSM152962 2 0.2973 0.65120 0.000 0.884 0.020 0.096
#> GSM152963 4 0.6010 0.23077 0.000 0.472 0.040 0.488
#> GSM152964 2 0.5420 0.30842 0.000 0.684 0.272 0.044
#> GSM152965 2 0.4744 0.55058 0.000 0.736 0.024 0.240
#> GSM152966 4 0.4835 0.74984 0.032 0.208 0.004 0.756
#> GSM152967 2 0.4464 0.59293 0.000 0.768 0.024 0.208
#> GSM152968 2 0.3108 0.64408 0.000 0.872 0.016 0.112
#> GSM152969 4 0.4798 0.74970 0.032 0.204 0.004 0.760
#> GSM152970 4 0.5279 0.74177 0.052 0.196 0.008 0.744
#> GSM152971 4 0.4887 0.74980 0.036 0.204 0.004 0.756
#> GSM152972 4 0.4733 0.73792 0.044 0.172 0.004 0.780
#> GSM152973 2 0.4086 0.58034 0.000 0.776 0.008 0.216
#> GSM152974 2 0.5050 0.50026 0.000 0.704 0.028 0.268
#> GSM152975 4 0.5937 0.45908 0.020 0.412 0.012 0.556
#> GSM152976 4 0.5112 0.73349 0.028 0.252 0.004 0.716
#> GSM152977 4 0.5693 0.72846 0.028 0.252 0.024 0.696
#> GSM152978 4 0.5461 0.70473 0.028 0.264 0.012 0.696
#> GSM152979 2 0.2313 0.63784 0.000 0.924 0.044 0.032
#> GSM152980 2 0.5766 -0.18706 0.004 0.512 0.020 0.464
#> GSM152981 2 0.4661 0.00830 0.000 0.652 0.348 0.000
#> GSM152982 4 0.5457 0.73387 0.028 0.248 0.016 0.708
#> GSM152983 4 0.4925 0.74948 0.036 0.208 0.004 0.752
#> GSM152984 2 0.4360 0.53271 0.000 0.744 0.008 0.248
#> GSM152985 4 0.4241 0.57772 0.088 0.056 0.016 0.840
#> GSM152986 4 0.4692 0.73972 0.040 0.176 0.004 0.780
#> GSM152987 1 0.6296 0.39788 0.548 0.000 0.064 0.388
#> GSM152988 2 0.3933 0.60907 0.000 0.792 0.008 0.200
#> GSM152989 4 0.4771 0.74791 0.036 0.192 0.004 0.768
#> GSM152990 2 0.2578 0.63443 0.000 0.912 0.052 0.036
#> GSM152991 2 0.4568 0.64285 0.000 0.800 0.076 0.124
#> GSM187524 1 0.0469 0.93223 0.988 0.000 0.000 0.012
#> GSM187525 1 0.0336 0.93301 0.992 0.000 0.000 0.008
#> GSM187526 1 0.0188 0.93400 0.996 0.000 0.000 0.004
#> GSM187527 1 0.1471 0.92206 0.960 0.012 0.004 0.024
#> GSM152856 1 0.1004 0.93411 0.972 0.000 0.004 0.024
#> GSM152857 1 0.1471 0.92206 0.960 0.012 0.004 0.024
#> GSM152858 1 0.0336 0.93301 0.992 0.000 0.000 0.008
#> GSM152859 1 0.6658 0.27909 0.508 0.008 0.420 0.064
#> GSM152860 1 0.0336 0.93301 0.992 0.000 0.000 0.008
#> GSM152861 1 0.0188 0.93400 0.996 0.000 0.000 0.004
#> GSM152862 1 0.0336 0.93301 0.992 0.000 0.000 0.008
#> GSM152863 1 0.0469 0.93596 0.988 0.000 0.000 0.012
#> GSM152864 1 0.0336 0.93629 0.992 0.000 0.000 0.008
#> GSM152865 1 0.0336 0.93629 0.992 0.000 0.000 0.008
#> GSM152866 1 0.0895 0.93481 0.976 0.000 0.004 0.020
#> GSM152867 1 0.0336 0.93629 0.992 0.000 0.000 0.008
#> GSM152868 1 0.0336 0.93629 0.992 0.000 0.000 0.008
#> GSM152869 1 0.0336 0.93629 0.992 0.000 0.000 0.008
#> GSM152870 1 0.0336 0.93301 0.992 0.000 0.000 0.008
#> GSM152871 1 0.0336 0.93301 0.992 0.000 0.000 0.008
#> GSM152872 1 0.0336 0.93301 0.992 0.000 0.000 0.008
#> GSM152873 1 0.1004 0.93411 0.972 0.000 0.004 0.024
#> GSM152874 1 0.1004 0.93411 0.972 0.000 0.004 0.024
#> GSM152875 1 0.1004 0.93411 0.972 0.000 0.004 0.024
#> GSM152876 1 0.1471 0.92206 0.960 0.012 0.004 0.024
#> GSM152877 1 0.1004 0.93411 0.972 0.000 0.004 0.024
#> GSM152878 1 0.1004 0.93411 0.972 0.000 0.004 0.024
#> GSM152879 1 0.1004 0.93411 0.972 0.000 0.004 0.024
#> GSM152880 1 0.1004 0.93411 0.972 0.000 0.004 0.024
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.1831 0.576146 0.000 0.920 0.076 0.000 0.004
#> GSM152805 3 0.4831 0.348065 0.000 0.068 0.740 0.016 0.176
#> GSM152806 3 0.4745 0.324311 0.000 0.060 0.744 0.016 0.180
#> GSM152807 2 0.1243 0.547157 0.000 0.960 0.028 0.008 0.004
#> GSM152808 3 0.4745 0.324311 0.000 0.060 0.744 0.016 0.180
#> GSM152809 2 0.1243 0.547157 0.000 0.960 0.028 0.008 0.004
#> GSM152810 5 0.4241 0.591483 0.000 0.012 0.264 0.008 0.716
#> GSM152811 5 0.4760 0.422427 0.000 0.020 0.416 0.000 0.564
#> GSM152812 2 0.1492 0.555551 0.000 0.948 0.040 0.008 0.004
#> GSM152813 2 0.3612 0.451821 0.000 0.764 0.228 0.008 0.000
#> GSM152814 2 0.1990 0.570367 0.000 0.920 0.068 0.008 0.004
#> GSM152815 2 0.1018 0.536290 0.000 0.968 0.016 0.016 0.000
#> GSM152816 3 0.4779 0.564303 0.000 0.340 0.628 0.000 0.032
#> GSM152817 3 0.4745 0.324311 0.000 0.060 0.744 0.016 0.180
#> GSM152818 3 0.4831 0.348065 0.000 0.068 0.740 0.016 0.176
#> GSM152819 3 0.5405 0.473497 0.000 0.380 0.556 0.000 0.064
#> GSM152820 2 0.4791 0.539425 0.000 0.736 0.160 0.100 0.004
#> GSM152821 2 0.2280 0.548892 0.000 0.880 0.120 0.000 0.000
#> GSM153115 2 0.4655 -0.002757 0.004 0.660 0.024 0.312 0.000
#> GSM153116 3 0.5610 0.596967 0.000 0.236 0.652 0.012 0.100
#> GSM153117 2 0.4973 -0.056792 0.000 0.564 0.408 0.004 0.024
#> GSM153118 2 0.2763 0.526647 0.000 0.848 0.148 0.000 0.004
#> GSM153119 3 0.5381 0.521223 0.000 0.128 0.724 0.040 0.108
#> GSM153120 2 0.4967 -0.539370 0.008 0.540 0.000 0.436 0.016
#> GSM153121 3 0.4286 0.614810 0.000 0.340 0.652 0.004 0.004
#> GSM153122 3 0.5207 0.359542 0.000 0.076 0.736 0.044 0.144
#> GSM153123 2 0.4470 0.033073 0.000 0.596 0.396 0.004 0.004
#> GSM153124 2 0.4789 0.457965 0.000 0.728 0.116 0.156 0.000
#> GSM153125 2 0.4655 -0.000697 0.004 0.660 0.024 0.312 0.000
#> GSM153126 3 0.4102 0.647202 0.000 0.300 0.692 0.004 0.004
#> GSM153127 2 0.1012 0.530007 0.000 0.968 0.012 0.020 0.000
#> GSM153128 3 0.5036 0.575805 0.000 0.372 0.592 0.004 0.032
#> GSM153129 2 0.4341 0.210292 0.000 0.628 0.364 0.008 0.000
#> GSM153130 3 0.4096 0.675987 0.000 0.260 0.724 0.004 0.012
#> GSM153131 2 0.4219 0.025158 0.000 0.584 0.416 0.000 0.000
#> GSM153132 2 0.4743 -0.233572 0.000 0.512 0.472 0.000 0.016
#> GSM153133 2 0.4101 0.172270 0.000 0.628 0.372 0.000 0.000
#> GSM153134 2 0.4302 0.255590 0.000 0.648 0.344 0.004 0.004
#> GSM153135 2 0.0833 0.522795 0.000 0.976 0.004 0.016 0.004
#> GSM153136 2 0.4402 -0.210690 0.004 0.620 0.004 0.372 0.000
#> GSM153137 2 0.2136 0.428867 0.000 0.904 0.000 0.088 0.008
#> GSM153138 2 0.1443 0.559164 0.000 0.948 0.044 0.004 0.004
#> GSM153139 3 0.4015 0.676250 0.000 0.264 0.724 0.004 0.008
#> GSM153140 2 0.4552 0.334205 0.000 0.668 0.308 0.020 0.004
#> GSM153141 2 0.1059 0.526370 0.000 0.968 0.008 0.020 0.004
#> GSM153142 3 0.4911 0.647768 0.000 0.196 0.720 0.008 0.076
#> GSM153143 2 0.2727 0.569266 0.000 0.868 0.116 0.016 0.000
#> GSM153144 2 0.4684 -0.082064 0.000 0.536 0.452 0.008 0.004
#> GSM153145 3 0.4745 0.324311 0.000 0.060 0.744 0.016 0.180
#> GSM153146 2 0.2563 0.549722 0.000 0.872 0.120 0.000 0.008
#> GSM153147 3 0.4452 0.216604 0.000 0.496 0.500 0.000 0.004
#> GSM153148 2 0.0798 0.530036 0.000 0.976 0.008 0.016 0.000
#> GSM153149 2 0.3838 0.358281 0.000 0.716 0.280 0.000 0.004
#> GSM153150 2 0.4970 -0.452745 0.004 0.560 0.016 0.416 0.004
#> GSM153151 2 0.4297 -0.215692 0.000 0.528 0.472 0.000 0.000
#> GSM153152 2 0.4287 -0.102811 0.000 0.540 0.460 0.000 0.000
#> GSM153153 2 0.3582 0.431143 0.000 0.768 0.224 0.000 0.008
#> GSM153154 2 0.4648 -0.188358 0.000 0.524 0.464 0.000 0.012
#> GSM153155 2 0.2890 0.527508 0.000 0.836 0.160 0.004 0.000
#> GSM153156 3 0.4045 0.600109 0.000 0.356 0.644 0.000 0.000
#> GSM153157 3 0.4281 0.634367 0.000 0.172 0.768 0.004 0.056
#> GSM153158 3 0.5114 0.480164 0.000 0.404 0.560 0.004 0.032
#> GSM153159 3 0.3881 0.674651 0.000 0.180 0.788 0.008 0.024
#> GSM153160 3 0.4059 0.653763 0.000 0.292 0.700 0.004 0.004
#> GSM153161 2 0.1569 0.500141 0.000 0.944 0.008 0.044 0.004
#> GSM153162 2 0.4572 -0.087177 0.000 0.540 0.452 0.004 0.004
#> GSM153163 3 0.3989 0.676259 0.000 0.260 0.728 0.004 0.008
#> GSM153164 2 0.4992 0.275461 0.000 0.640 0.320 0.028 0.012
#> GSM153165 3 0.3814 0.669811 0.000 0.276 0.720 0.000 0.004
#> GSM153166 2 0.4063 0.368664 0.000 0.708 0.280 0.012 0.000
#> GSM153167 2 0.4318 0.245072 0.000 0.644 0.348 0.004 0.004
#> GSM153168 3 0.4780 0.320325 0.000 0.060 0.740 0.016 0.184
#> GSM153169 3 0.4291 0.675859 0.000 0.276 0.704 0.004 0.016
#> GSM153170 3 0.4009 0.645855 0.000 0.312 0.684 0.000 0.004
#> GSM153171 2 0.4887 0.198678 0.008 0.692 0.048 0.252 0.000
#> GSM153172 2 0.3160 0.483941 0.000 0.808 0.188 0.004 0.000
#> GSM153173 3 0.3814 0.669811 0.000 0.276 0.720 0.000 0.004
#> GSM153174 2 0.4675 -0.053774 0.000 0.544 0.444 0.008 0.004
#> GSM153175 2 0.5255 0.108019 0.004 0.644 0.068 0.284 0.000
#> GSM153176 2 0.5621 0.216317 0.004 0.632 0.112 0.252 0.000
#> GSM153177 2 0.4884 0.019506 0.000 0.584 0.392 0.008 0.016
#> GSM152931 2 0.4709 -0.042878 0.004 0.648 0.024 0.324 0.000
#> GSM152932 2 0.3489 0.465761 0.000 0.784 0.208 0.004 0.004
#> GSM152933 2 0.2806 0.527176 0.000 0.844 0.152 0.000 0.004
#> GSM152934 2 0.4851 0.524258 0.000 0.712 0.196 0.092 0.000
#> GSM152935 2 0.4980 -0.053833 0.000 0.576 0.396 0.020 0.008
#> GSM152936 2 0.4631 0.208492 0.004 0.704 0.040 0.252 0.000
#> GSM152937 3 0.4657 0.542709 0.000 0.380 0.604 0.008 0.008
#> GSM152938 3 0.4564 0.525952 0.000 0.388 0.600 0.004 0.008
#> GSM152939 2 0.5091 0.195209 0.000 0.584 0.372 0.044 0.000
#> GSM152940 4 0.5383 0.574203 0.020 0.432 0.004 0.528 0.016
#> GSM152941 1 0.6861 0.074712 0.512 0.144 0.000 0.308 0.036
#> GSM152942 3 0.4798 0.383548 0.000 0.440 0.540 0.020 0.000
#> GSM152943 2 0.2494 0.497966 0.000 0.904 0.032 0.056 0.008
#> GSM152944 3 0.4252 0.675361 0.000 0.280 0.700 0.000 0.020
#> GSM152945 2 0.8258 -0.165650 0.000 0.360 0.168 0.304 0.168
#> GSM152946 2 0.4822 0.490110 0.000 0.704 0.220 0.076 0.000
#> GSM152947 2 0.5212 -0.441288 0.020 0.548 0.016 0.416 0.000
#> GSM152948 2 0.2540 0.571642 0.000 0.888 0.088 0.024 0.000
#> GSM152949 2 0.4591 -0.165776 0.000 0.516 0.476 0.004 0.004
#> GSM152950 2 0.4450 -0.250382 0.000 0.508 0.488 0.000 0.004
#> GSM152951 2 0.2824 0.574432 0.000 0.864 0.116 0.020 0.000
#> GSM152952 2 0.0955 0.517902 0.000 0.968 0.004 0.028 0.000
#> GSM152953 2 0.1518 0.563204 0.000 0.944 0.048 0.004 0.004
#> GSM152954 2 0.4469 0.171635 0.016 0.724 0.012 0.244 0.004
#> GSM152955 2 0.3960 0.557200 0.000 0.800 0.140 0.056 0.004
#> GSM152956 2 0.0932 0.519416 0.000 0.972 0.004 0.020 0.004
#> GSM152957 2 0.4822 -0.112476 0.008 0.628 0.020 0.344 0.000
#> GSM152958 2 0.4402 -0.212323 0.004 0.620 0.004 0.372 0.000
#> GSM152959 2 0.4879 -0.267993 0.020 0.612 0.008 0.360 0.000
#> GSM152960 2 0.4942 -0.226507 0.020 0.632 0.008 0.336 0.004
#> GSM152961 4 0.4803 0.536707 0.012 0.488 0.004 0.496 0.000
#> GSM152962 3 0.4594 0.330948 0.000 0.484 0.508 0.004 0.004
#> GSM152963 2 0.0693 0.519112 0.000 0.980 0.000 0.012 0.008
#> GSM152964 3 0.6870 0.465795 0.000 0.220 0.568 0.056 0.156
#> GSM152965 2 0.4108 0.296174 0.000 0.684 0.308 0.008 0.000
#> GSM152966 2 0.4553 -0.048637 0.004 0.652 0.016 0.328 0.000
#> GSM152967 2 0.4225 0.190305 0.000 0.632 0.364 0.000 0.004
#> GSM152968 2 0.4452 -0.225091 0.000 0.500 0.496 0.000 0.004
#> GSM152969 2 0.4457 -0.046915 0.004 0.656 0.012 0.328 0.000
#> GSM152970 2 0.4786 -0.136690 0.012 0.620 0.012 0.356 0.000
#> GSM152971 2 0.4387 -0.081590 0.004 0.652 0.008 0.336 0.000
#> GSM152972 2 0.4389 -0.194692 0.004 0.624 0.004 0.368 0.000
#> GSM152973 2 0.4937 -0.009620 0.000 0.544 0.428 0.028 0.000
#> GSM152974 2 0.4015 0.372753 0.000 0.708 0.284 0.004 0.004
#> GSM152975 2 0.5322 0.428007 0.000 0.684 0.128 0.184 0.004
#> GSM152976 2 0.5053 0.027515 0.004 0.644 0.048 0.304 0.000
#> GSM152977 2 0.5197 0.046064 0.004 0.652 0.044 0.292 0.008
#> GSM152978 2 0.4243 0.177675 0.016 0.732 0.004 0.244 0.004
#> GSM152979 3 0.4236 0.627490 0.000 0.328 0.664 0.004 0.004
#> GSM152980 2 0.4841 0.536201 0.000 0.732 0.160 0.104 0.004
#> GSM152981 3 0.4780 0.320325 0.000 0.060 0.740 0.016 0.184
#> GSM152982 2 0.5185 0.023473 0.004 0.644 0.048 0.300 0.004
#> GSM152983 2 0.4625 -0.077777 0.004 0.652 0.020 0.324 0.000
#> GSM152984 2 0.4980 0.164865 0.000 0.584 0.380 0.036 0.000
#> GSM152985 4 0.5192 0.558046 0.032 0.476 0.004 0.488 0.000
#> GSM152986 2 0.4375 -0.177609 0.004 0.628 0.004 0.364 0.000
#> GSM152987 4 0.6434 -0.288853 0.352 0.040 0.004 0.536 0.068
#> GSM152988 2 0.4966 0.074839 0.000 0.564 0.404 0.032 0.000
#> GSM152989 2 0.4763 -0.137364 0.008 0.624 0.016 0.352 0.000
#> GSM152990 3 0.4333 0.601374 0.000 0.352 0.640 0.004 0.004
#> GSM152991 3 0.5084 0.321594 0.000 0.484 0.488 0.008 0.020
#> GSM187524 1 0.1364 0.915370 0.952 0.000 0.000 0.012 0.036
#> GSM187525 1 0.1251 0.917835 0.956 0.000 0.000 0.008 0.036
#> GSM187526 1 0.1168 0.920239 0.960 0.000 0.000 0.008 0.032
#> GSM187527 1 0.2002 0.919528 0.932 0.020 0.000 0.020 0.028
#> GSM152856 1 0.1686 0.932283 0.944 0.008 0.000 0.020 0.028
#> GSM152857 1 0.2002 0.919528 0.932 0.020 0.000 0.020 0.028
#> GSM152858 1 0.0510 0.933833 0.984 0.000 0.000 0.000 0.016
#> GSM152859 5 0.4684 -0.110319 0.452 0.000 0.004 0.008 0.536
#> GSM152860 1 0.0510 0.933833 0.984 0.000 0.000 0.000 0.016
#> GSM152861 1 0.0404 0.934697 0.988 0.000 0.000 0.000 0.012
#> GSM152862 1 0.0510 0.933833 0.984 0.000 0.000 0.000 0.016
#> GSM152863 1 0.0451 0.938528 0.988 0.000 0.000 0.008 0.004
#> GSM152864 1 0.0162 0.938538 0.996 0.000 0.000 0.004 0.000
#> GSM152865 1 0.0162 0.938538 0.996 0.000 0.000 0.004 0.000
#> GSM152866 1 0.1503 0.934146 0.952 0.008 0.000 0.020 0.020
#> GSM152867 1 0.0162 0.938538 0.996 0.000 0.000 0.004 0.000
#> GSM152868 1 0.0162 0.938538 0.996 0.000 0.000 0.004 0.000
#> GSM152869 1 0.0162 0.938538 0.996 0.000 0.000 0.004 0.000
#> GSM152870 1 0.0510 0.933833 0.984 0.000 0.000 0.000 0.016
#> GSM152871 1 0.0510 0.933833 0.984 0.000 0.000 0.000 0.016
#> GSM152872 1 0.0510 0.933833 0.984 0.000 0.000 0.000 0.016
#> GSM152873 1 0.1686 0.932283 0.944 0.008 0.000 0.020 0.028
#> GSM152874 1 0.1686 0.932283 0.944 0.008 0.000 0.020 0.028
#> GSM152875 1 0.1686 0.932283 0.944 0.008 0.000 0.020 0.028
#> GSM152876 1 0.2002 0.919528 0.932 0.020 0.000 0.020 0.028
#> GSM152877 1 0.1686 0.932283 0.944 0.008 0.000 0.020 0.028
#> GSM152878 1 0.1686 0.932283 0.944 0.008 0.000 0.020 0.028
#> GSM152879 1 0.1686 0.932283 0.944 0.008 0.000 0.020 0.028
#> GSM152880 1 0.1686 0.932283 0.944 0.008 0.000 0.020 0.028
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.1757 0.5490 0.000 0.916 0.076 0.000 0.008 0.000
#> GSM152805 3 0.4203 0.1272 0.000 0.032 0.652 0.000 0.316 0.000
#> GSM152806 3 0.3938 0.0669 0.000 0.016 0.660 0.000 0.324 0.000
#> GSM152807 2 0.1116 0.5227 0.000 0.960 0.028 0.008 0.004 0.000
#> GSM152808 3 0.3938 0.0669 0.000 0.016 0.660 0.000 0.324 0.000
#> GSM152809 2 0.1116 0.5227 0.000 0.960 0.028 0.008 0.004 0.000
#> GSM152810 5 0.3734 0.2188 0.000 0.000 0.164 0.012 0.784 0.040
#> GSM152811 5 0.4613 0.2731 0.000 0.008 0.308 0.004 0.644 0.036
#> GSM152812 2 0.1340 0.5305 0.000 0.948 0.040 0.008 0.004 0.000
#> GSM152813 2 0.3302 0.4322 0.000 0.760 0.232 0.004 0.004 0.000
#> GSM152814 2 0.1787 0.5424 0.000 0.920 0.068 0.008 0.004 0.000
#> GSM152815 2 0.0914 0.5132 0.000 0.968 0.016 0.016 0.000 0.000
#> GSM152816 3 0.4775 0.5192 0.000 0.284 0.632 0.000 0.084 0.000
#> GSM152817 3 0.3938 0.0669 0.000 0.016 0.660 0.000 0.324 0.000
#> GSM152818 3 0.4203 0.1272 0.000 0.032 0.652 0.000 0.316 0.000
#> GSM152819 3 0.5345 0.4121 0.000 0.364 0.520 0.000 0.116 0.000
#> GSM152820 2 0.4670 0.4977 0.000 0.704 0.176 0.112 0.008 0.000
#> GSM152821 2 0.2234 0.5478 0.000 0.872 0.124 0.000 0.004 0.000
#> GSM153115 2 0.4199 -0.0186 0.004 0.640 0.020 0.336 0.000 0.000
#> GSM153116 3 0.5170 0.4775 0.000 0.204 0.620 0.000 0.176 0.000
#> GSM153117 2 0.4709 -0.1353 0.000 0.540 0.412 0.000 0.048 0.000
#> GSM153118 2 0.2692 0.5220 0.000 0.840 0.148 0.000 0.012 0.000
#> GSM153119 3 0.5667 0.3201 0.000 0.076 0.676 0.024 0.164 0.060
#> GSM153120 2 0.4515 -0.5534 0.004 0.516 0.000 0.460 0.004 0.016
#> GSM153121 3 0.3784 0.5887 0.000 0.308 0.680 0.000 0.012 0.000
#> GSM153122 3 0.5611 0.0517 0.000 0.024 0.648 0.032 0.224 0.072
#> GSM153123 2 0.4032 -0.0759 0.000 0.572 0.420 0.000 0.008 0.000
#> GSM153124 2 0.4651 0.4199 0.000 0.700 0.124 0.172 0.004 0.000
#> GSM153125 2 0.4360 -0.0184 0.004 0.628 0.028 0.340 0.000 0.000
#> GSM153126 3 0.3398 0.6136 0.000 0.252 0.740 0.000 0.008 0.000
#> GSM153127 2 0.0909 0.5076 0.000 0.968 0.012 0.020 0.000 0.000
#> GSM153128 3 0.4659 0.5570 0.000 0.336 0.612 0.000 0.048 0.004
#> GSM153129 2 0.4109 0.1082 0.000 0.596 0.392 0.008 0.004 0.000
#> GSM153130 3 0.3201 0.6320 0.000 0.208 0.780 0.000 0.012 0.000
#> GSM153131 2 0.4147 -0.0677 0.000 0.552 0.436 0.000 0.012 0.000
#> GSM153132 3 0.4258 0.3196 0.000 0.468 0.516 0.000 0.016 0.000
#> GSM153133 2 0.4024 0.0669 0.000 0.592 0.400 0.000 0.004 0.004
#> GSM153134 2 0.4058 0.1683 0.000 0.616 0.372 0.004 0.008 0.000
#> GSM153135 2 0.0748 0.5000 0.000 0.976 0.004 0.016 0.004 0.000
#> GSM153136 2 0.4015 -0.1846 0.004 0.596 0.004 0.396 0.000 0.000
#> GSM153137 2 0.2020 0.3976 0.000 0.896 0.000 0.096 0.008 0.000
#> GSM153138 2 0.1668 0.5378 0.000 0.928 0.060 0.008 0.004 0.000
#> GSM153139 3 0.3133 0.6325 0.000 0.212 0.780 0.000 0.008 0.000
#> GSM153140 2 0.4304 0.2623 0.000 0.636 0.336 0.020 0.008 0.000
#> GSM153141 2 0.1053 0.5063 0.000 0.964 0.012 0.020 0.004 0.000
#> GSM153142 3 0.4427 0.5386 0.000 0.148 0.716 0.000 0.136 0.000
#> GSM153143 2 0.2664 0.5535 0.000 0.848 0.136 0.016 0.000 0.000
#> GSM153144 2 0.4225 -0.1932 0.000 0.508 0.480 0.008 0.004 0.000
#> GSM153145 3 0.3938 0.0669 0.000 0.016 0.660 0.000 0.324 0.000
#> GSM153146 2 0.2446 0.5468 0.000 0.864 0.124 0.000 0.012 0.000
#> GSM153147 3 0.4089 0.2930 0.000 0.468 0.524 0.000 0.008 0.000
#> GSM153148 2 0.0717 0.5068 0.000 0.976 0.008 0.016 0.000 0.000
#> GSM153149 2 0.3672 0.3017 0.000 0.688 0.304 0.000 0.008 0.000
#> GSM153150 2 0.4289 -0.4437 0.000 0.540 0.012 0.444 0.004 0.000
#> GSM153151 3 0.3999 0.2707 0.000 0.496 0.500 0.000 0.004 0.000
#> GSM153152 2 0.3868 -0.2120 0.000 0.508 0.492 0.000 0.000 0.000
#> GSM153153 2 0.3368 0.4029 0.000 0.756 0.232 0.000 0.012 0.000
#> GSM153154 3 0.4183 0.2913 0.000 0.480 0.508 0.000 0.012 0.000
#> GSM153155 2 0.2920 0.5180 0.000 0.820 0.168 0.004 0.008 0.000
#> GSM153156 3 0.3619 0.5822 0.000 0.316 0.680 0.000 0.004 0.000
#> GSM153157 3 0.3888 0.5050 0.000 0.108 0.780 0.000 0.108 0.004
#> GSM153158 3 0.4727 0.4777 0.000 0.368 0.576 0.000 0.056 0.000
#> GSM153159 3 0.3336 0.5934 0.000 0.132 0.812 0.000 0.056 0.000
#> GSM153160 3 0.3349 0.6175 0.000 0.244 0.748 0.000 0.008 0.000
#> GSM153161 2 0.1523 0.4782 0.000 0.940 0.008 0.044 0.008 0.000
#> GSM153162 2 0.4127 -0.2048 0.000 0.508 0.484 0.004 0.004 0.000
#> GSM153163 3 0.3103 0.6321 0.000 0.208 0.784 0.000 0.008 0.000
#> GSM153164 2 0.4708 0.2212 0.000 0.612 0.340 0.032 0.016 0.000
#> GSM153165 3 0.3109 0.6294 0.000 0.224 0.772 0.000 0.004 0.000
#> GSM153166 2 0.3733 0.3335 0.000 0.700 0.288 0.008 0.004 0.000
#> GSM153167 2 0.4069 0.1592 0.000 0.612 0.376 0.004 0.008 0.000
#> GSM153168 3 0.3953 0.0615 0.000 0.016 0.656 0.000 0.328 0.000
#> GSM153169 3 0.3599 0.6332 0.000 0.220 0.756 0.000 0.020 0.004
#> GSM153170 3 0.3337 0.6155 0.000 0.260 0.736 0.000 0.004 0.000
#> GSM153171 2 0.4411 0.1688 0.004 0.672 0.048 0.276 0.000 0.000
#> GSM153172 2 0.2730 0.4717 0.000 0.808 0.192 0.000 0.000 0.000
#> GSM153173 3 0.3109 0.6294 0.000 0.224 0.772 0.000 0.004 0.000
#> GSM153174 2 0.4224 -0.1747 0.000 0.512 0.476 0.008 0.004 0.000
#> GSM153175 2 0.4925 0.0741 0.004 0.624 0.068 0.300 0.004 0.000
#> GSM153176 2 0.5183 0.1843 0.004 0.608 0.116 0.272 0.000 0.000
#> GSM153177 2 0.4625 -0.0958 0.000 0.544 0.424 0.004 0.024 0.004
#> GSM152931 2 0.4328 -0.0497 0.004 0.620 0.024 0.352 0.000 0.000
#> GSM152932 2 0.3329 0.4289 0.000 0.756 0.236 0.004 0.004 0.000
#> GSM152933 2 0.2730 0.5227 0.000 0.836 0.152 0.000 0.012 0.000
#> GSM152934 2 0.4756 0.5015 0.000 0.684 0.212 0.096 0.008 0.000
#> GSM152935 2 0.4852 -0.0792 0.000 0.560 0.396 0.016 0.024 0.004
#> GSM152936 2 0.4488 0.1659 0.004 0.664 0.052 0.280 0.000 0.000
#> GSM152937 3 0.4289 0.5403 0.000 0.340 0.636 0.004 0.012 0.008
#> GSM152938 3 0.4148 0.5286 0.000 0.344 0.636 0.000 0.016 0.004
#> GSM152939 2 0.4751 0.1284 0.000 0.560 0.392 0.044 0.004 0.000
#> GSM152940 4 0.4394 0.5459 0.004 0.408 0.000 0.568 0.000 0.020
#> GSM152941 1 0.7206 -0.2319 0.444 0.128 0.000 0.316 0.024 0.088
#> GSM152942 3 0.4269 0.4149 0.000 0.412 0.568 0.020 0.000 0.000
#> GSM152943 2 0.2588 0.4772 0.000 0.888 0.040 0.060 0.008 0.004
#> GSM152944 3 0.3514 0.6341 0.000 0.228 0.752 0.000 0.020 0.000
#> GSM152945 4 0.7991 -0.4520 0.000 0.240 0.060 0.380 0.088 0.232
#> GSM152946 2 0.4640 0.4756 0.000 0.676 0.240 0.080 0.004 0.000
#> GSM152947 2 0.4478 -0.4457 0.008 0.524 0.016 0.452 0.000 0.000
#> GSM152948 2 0.2510 0.5462 0.000 0.872 0.100 0.028 0.000 0.000
#> GSM152949 3 0.4127 0.2423 0.000 0.484 0.508 0.004 0.004 0.000
#> GSM152950 3 0.4308 0.3168 0.000 0.468 0.516 0.000 0.012 0.004
#> GSM152951 2 0.2909 0.5549 0.000 0.836 0.136 0.028 0.000 0.000
#> GSM152952 2 0.0858 0.4951 0.000 0.968 0.004 0.028 0.000 0.000
#> GSM152953 2 0.1615 0.5423 0.000 0.928 0.064 0.004 0.004 0.000
#> GSM152954 2 0.4064 0.1574 0.012 0.704 0.012 0.268 0.004 0.000
#> GSM152955 2 0.4034 0.5173 0.000 0.772 0.152 0.064 0.008 0.004
#> GSM152956 2 0.0837 0.4964 0.000 0.972 0.004 0.020 0.004 0.000
#> GSM152957 2 0.4382 -0.1061 0.008 0.612 0.020 0.360 0.000 0.000
#> GSM152958 2 0.4015 -0.1859 0.004 0.596 0.004 0.396 0.000 0.000
#> GSM152959 2 0.4387 -0.2665 0.016 0.584 0.008 0.392 0.000 0.000
#> GSM152960 2 0.4450 -0.2392 0.016 0.608 0.008 0.364 0.004 0.000
#> GSM152961 4 0.4086 0.5129 0.008 0.464 0.000 0.528 0.000 0.000
#> GSM152962 3 0.4431 0.3722 0.000 0.456 0.524 0.004 0.012 0.004
#> GSM152963 2 0.0622 0.4966 0.000 0.980 0.000 0.012 0.008 0.000
#> GSM152964 3 0.6954 0.2728 0.000 0.172 0.512 0.056 0.232 0.028
#> GSM152965 2 0.3925 0.2262 0.000 0.656 0.332 0.008 0.004 0.000
#> GSM152966 2 0.4187 -0.0646 0.004 0.624 0.016 0.356 0.000 0.000
#> GSM152967 2 0.3872 0.0998 0.000 0.604 0.392 0.000 0.004 0.000
#> GSM152968 3 0.3982 0.3091 0.000 0.460 0.536 0.000 0.004 0.000
#> GSM152969 2 0.4102 -0.0617 0.004 0.628 0.012 0.356 0.000 0.000
#> GSM152970 2 0.4171 -0.1225 0.004 0.604 0.012 0.380 0.000 0.000
#> GSM152971 2 0.4022 -0.0815 0.004 0.628 0.008 0.360 0.000 0.000
#> GSM152972 2 0.4006 -0.1776 0.004 0.600 0.004 0.392 0.000 0.000
#> GSM152973 2 0.4588 -0.0864 0.000 0.520 0.448 0.028 0.004 0.000
#> GSM152974 2 0.3684 0.3278 0.000 0.692 0.300 0.004 0.004 0.000
#> GSM152975 2 0.4981 0.3866 0.000 0.656 0.132 0.208 0.004 0.000
#> GSM152976 2 0.4673 0.0219 0.004 0.620 0.052 0.324 0.000 0.000
#> GSM152977 2 0.4845 0.0268 0.004 0.628 0.044 0.312 0.012 0.000
#> GSM152978 2 0.3947 0.1704 0.012 0.712 0.008 0.264 0.004 0.000
#> GSM152979 3 0.3448 0.6031 0.000 0.280 0.716 0.000 0.004 0.000
#> GSM152980 2 0.4750 0.4914 0.000 0.696 0.176 0.120 0.008 0.000
#> GSM152981 3 0.3953 0.0615 0.000 0.016 0.656 0.000 0.328 0.000
#> GSM152982 2 0.4912 -0.0187 0.004 0.612 0.052 0.324 0.008 0.000
#> GSM152983 2 0.4254 -0.0820 0.004 0.624 0.020 0.352 0.000 0.000
#> GSM152984 2 0.4641 0.1064 0.000 0.564 0.396 0.036 0.004 0.000
#> GSM152985 4 0.4591 0.5313 0.028 0.452 0.000 0.516 0.004 0.000
#> GSM152986 2 0.4006 -0.1766 0.004 0.600 0.004 0.392 0.000 0.000
#> GSM152987 6 0.5225 0.0000 0.080 0.000 0.000 0.284 0.020 0.616
#> GSM152988 2 0.4682 -0.0125 0.000 0.540 0.420 0.036 0.004 0.000
#> GSM152989 2 0.4326 -0.1288 0.008 0.608 0.016 0.368 0.000 0.000
#> GSM152990 3 0.3653 0.5887 0.000 0.300 0.692 0.000 0.008 0.000
#> GSM152991 3 0.4881 0.3469 0.000 0.452 0.496 0.000 0.048 0.004
#> GSM187524 1 0.2619 0.8433 0.884 0.000 0.000 0.012 0.048 0.056
#> GSM187525 1 0.2553 0.8466 0.888 0.000 0.000 0.012 0.044 0.056
#> GSM187526 1 0.2485 0.8493 0.892 0.000 0.000 0.012 0.040 0.056
#> GSM187527 1 0.2361 0.8790 0.880 0.012 0.000 0.004 0.000 0.104
#> GSM152856 1 0.2006 0.8894 0.892 0.000 0.000 0.004 0.000 0.104
#> GSM152857 1 0.2361 0.8790 0.880 0.012 0.000 0.004 0.000 0.104
#> GSM152858 1 0.0972 0.8905 0.964 0.000 0.000 0.000 0.028 0.008
#> GSM152859 5 0.5201 -0.2012 0.424 0.000 0.000 0.020 0.508 0.048
#> GSM152860 1 0.0972 0.8905 0.964 0.000 0.000 0.000 0.028 0.008
#> GSM152861 1 0.0891 0.8926 0.968 0.000 0.000 0.000 0.024 0.008
#> GSM152862 1 0.0972 0.8905 0.964 0.000 0.000 0.000 0.028 0.008
#> GSM152863 1 0.0405 0.9008 0.988 0.000 0.000 0.004 0.000 0.008
#> GSM152864 1 0.0146 0.9005 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM152865 1 0.0146 0.9005 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM152866 1 0.1858 0.8924 0.904 0.000 0.000 0.004 0.000 0.092
#> GSM152867 1 0.0146 0.9005 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM152868 1 0.0146 0.9005 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM152869 1 0.0146 0.9005 0.996 0.000 0.000 0.004 0.000 0.000
#> GSM152870 1 0.0972 0.8905 0.964 0.000 0.000 0.000 0.028 0.008
#> GSM152871 1 0.0972 0.8905 0.964 0.000 0.000 0.000 0.028 0.008
#> GSM152872 1 0.0972 0.8905 0.964 0.000 0.000 0.000 0.028 0.008
#> GSM152873 1 0.2006 0.8894 0.892 0.000 0.000 0.004 0.000 0.104
#> GSM152874 1 0.2006 0.8894 0.892 0.000 0.000 0.004 0.000 0.104
#> GSM152875 1 0.2006 0.8894 0.892 0.000 0.000 0.004 0.000 0.104
#> GSM152876 1 0.2361 0.8790 0.880 0.012 0.000 0.004 0.000 0.104
#> GSM152877 1 0.2006 0.8894 0.892 0.000 0.000 0.004 0.000 0.104
#> GSM152878 1 0.2006 0.8894 0.892 0.000 0.000 0.004 0.000 0.104
#> GSM152879 1 0.2006 0.8894 0.892 0.000 0.000 0.004 0.000 0.104
#> GSM152880 1 0.2006 0.8894 0.892 0.000 0.000 0.004 0.000 0.104
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> MAD:hclust 142 4.59e-22 2
#> MAD:hclust 138 4.21e-25 3
#> MAD:hclust 116 1.38e-31 4
#> MAD:hclust 83 2.78e-15 5
#> MAD:hclust 73 9.16e-14 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "kmeans"]
# you can also extract it by
# res = res_list["MAD:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.989 0.966 0.985 0.3371 0.673 0.673
#> 3 3 0.755 0.879 0.931 0.8325 0.658 0.507
#> 4 4 0.635 0.687 0.774 0.1461 0.799 0.514
#> 5 5 0.697 0.791 0.829 0.0782 0.892 0.627
#> 6 6 0.703 0.729 0.809 0.0410 0.981 0.914
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.9846 0.000 1.000
#> GSM152805 2 0.0000 0.9846 0.000 1.000
#> GSM152806 2 0.0000 0.9846 0.000 1.000
#> GSM152807 2 0.0000 0.9846 0.000 1.000
#> GSM152808 2 0.0000 0.9846 0.000 1.000
#> GSM152809 2 0.0000 0.9846 0.000 1.000
#> GSM152810 2 0.0000 0.9846 0.000 1.000
#> GSM152811 2 0.0000 0.9846 0.000 1.000
#> GSM152812 2 0.0000 0.9846 0.000 1.000
#> GSM152813 2 0.0000 0.9846 0.000 1.000
#> GSM152814 2 0.0000 0.9846 0.000 1.000
#> GSM152815 2 0.0000 0.9846 0.000 1.000
#> GSM152816 2 0.0000 0.9846 0.000 1.000
#> GSM152817 2 0.0000 0.9846 0.000 1.000
#> GSM152818 2 0.0000 0.9846 0.000 1.000
#> GSM152819 2 0.0000 0.9846 0.000 1.000
#> GSM152820 2 0.0000 0.9846 0.000 1.000
#> GSM152821 2 0.0000 0.9846 0.000 1.000
#> GSM153115 2 0.1843 0.9644 0.028 0.972
#> GSM153116 2 0.0000 0.9846 0.000 1.000
#> GSM153117 2 0.0000 0.9846 0.000 1.000
#> GSM153118 2 0.0000 0.9846 0.000 1.000
#> GSM153119 2 0.0000 0.9846 0.000 1.000
#> GSM153120 2 0.4690 0.8936 0.100 0.900
#> GSM153121 2 0.0000 0.9846 0.000 1.000
#> GSM153122 2 0.0000 0.9846 0.000 1.000
#> GSM153123 2 0.0000 0.9846 0.000 1.000
#> GSM153124 2 0.0000 0.9846 0.000 1.000
#> GSM153125 2 0.0938 0.9766 0.012 0.988
#> GSM153126 2 0.0000 0.9846 0.000 1.000
#> GSM153127 2 0.0000 0.9846 0.000 1.000
#> GSM153128 2 0.0000 0.9846 0.000 1.000
#> GSM153129 2 0.0000 0.9846 0.000 1.000
#> GSM153130 2 0.0000 0.9846 0.000 1.000
#> GSM153131 2 0.0000 0.9846 0.000 1.000
#> GSM153132 2 0.0000 0.9846 0.000 1.000
#> GSM153133 2 0.0000 0.9846 0.000 1.000
#> GSM153134 2 0.0000 0.9846 0.000 1.000
#> GSM153135 2 0.0000 0.9846 0.000 1.000
#> GSM153136 2 0.1633 0.9676 0.024 0.976
#> GSM153137 2 0.0000 0.9846 0.000 1.000
#> GSM153138 2 0.0000 0.9846 0.000 1.000
#> GSM153139 2 0.0000 0.9846 0.000 1.000
#> GSM153140 2 0.0000 0.9846 0.000 1.000
#> GSM153141 2 0.0000 0.9846 0.000 1.000
#> GSM153142 2 0.0000 0.9846 0.000 1.000
#> GSM153143 2 0.0000 0.9846 0.000 1.000
#> GSM153144 2 0.0000 0.9846 0.000 1.000
#> GSM153145 2 0.0000 0.9846 0.000 1.000
#> GSM153146 2 0.0000 0.9846 0.000 1.000
#> GSM153147 2 0.0000 0.9846 0.000 1.000
#> GSM153148 2 0.0000 0.9846 0.000 1.000
#> GSM153149 2 0.0000 0.9846 0.000 1.000
#> GSM153150 2 0.4815 0.8887 0.104 0.896
#> GSM153151 2 0.0000 0.9846 0.000 1.000
#> GSM153152 2 0.0000 0.9846 0.000 1.000
#> GSM153153 2 0.0000 0.9846 0.000 1.000
#> GSM153154 2 0.0000 0.9846 0.000 1.000
#> GSM153155 2 0.0000 0.9846 0.000 1.000
#> GSM153156 2 0.0000 0.9846 0.000 1.000
#> GSM153157 2 0.0000 0.9846 0.000 1.000
#> GSM153158 2 0.0000 0.9846 0.000 1.000
#> GSM153159 2 0.0000 0.9846 0.000 1.000
#> GSM153160 2 0.0000 0.9846 0.000 1.000
#> GSM153161 2 0.0000 0.9846 0.000 1.000
#> GSM153162 2 0.0000 0.9846 0.000 1.000
#> GSM153163 2 0.0000 0.9846 0.000 1.000
#> GSM153164 2 0.0000 0.9846 0.000 1.000
#> GSM153165 2 0.0000 0.9846 0.000 1.000
#> GSM153166 2 0.0000 0.9846 0.000 1.000
#> GSM153167 2 0.0000 0.9846 0.000 1.000
#> GSM153168 2 0.0000 0.9846 0.000 1.000
#> GSM153169 2 0.0000 0.9846 0.000 1.000
#> GSM153170 2 0.0000 0.9846 0.000 1.000
#> GSM153171 2 0.5059 0.8796 0.112 0.888
#> GSM153172 2 0.0000 0.9846 0.000 1.000
#> GSM153173 2 0.0000 0.9846 0.000 1.000
#> GSM153174 2 0.0000 0.9846 0.000 1.000
#> GSM153175 2 0.0376 0.9821 0.004 0.996
#> GSM153176 2 0.1414 0.9707 0.020 0.980
#> GSM153177 2 0.0000 0.9846 0.000 1.000
#> GSM152931 2 0.0672 0.9794 0.008 0.992
#> GSM152932 2 0.0000 0.9846 0.000 1.000
#> GSM152933 2 0.0000 0.9846 0.000 1.000
#> GSM152934 2 0.0000 0.9846 0.000 1.000
#> GSM152935 2 0.0000 0.9846 0.000 1.000
#> GSM152936 2 0.1184 0.9737 0.016 0.984
#> GSM152937 2 0.0000 0.9846 0.000 1.000
#> GSM152938 2 0.0000 0.9846 0.000 1.000
#> GSM152939 2 0.0376 0.9821 0.004 0.996
#> GSM152940 2 0.9988 0.0913 0.480 0.520
#> GSM152941 1 0.0000 0.9838 1.000 0.000
#> GSM152942 2 0.0000 0.9846 0.000 1.000
#> GSM152943 2 0.0000 0.9846 0.000 1.000
#> GSM152944 2 0.0000 0.9846 0.000 1.000
#> GSM152945 2 0.0000 0.9846 0.000 1.000
#> GSM152946 2 0.0000 0.9846 0.000 1.000
#> GSM152947 2 0.6048 0.8352 0.148 0.852
#> GSM152948 2 0.0000 0.9846 0.000 1.000
#> GSM152949 2 0.0000 0.9846 0.000 1.000
#> GSM152950 2 0.0000 0.9846 0.000 1.000
#> GSM152951 2 0.0000 0.9846 0.000 1.000
#> GSM152952 2 0.0000 0.9846 0.000 1.000
#> GSM152953 2 0.0000 0.9846 0.000 1.000
#> GSM152954 2 0.2236 0.9576 0.036 0.964
#> GSM152955 2 0.0000 0.9846 0.000 1.000
#> GSM152956 2 0.0000 0.9846 0.000 1.000
#> GSM152957 2 0.4161 0.9107 0.084 0.916
#> GSM152958 1 0.9552 0.3773 0.624 0.376
#> GSM152959 2 0.7376 0.7505 0.208 0.792
#> GSM152960 2 0.1633 0.9676 0.024 0.976
#> GSM152961 1 0.6247 0.8052 0.844 0.156
#> GSM152962 2 0.0000 0.9846 0.000 1.000
#> GSM152963 2 0.0000 0.9846 0.000 1.000
#> GSM152964 2 0.0000 0.9846 0.000 1.000
#> GSM152965 2 0.0000 0.9846 0.000 1.000
#> GSM152966 2 0.1633 0.9676 0.024 0.976
#> GSM152967 2 0.0000 0.9846 0.000 1.000
#> GSM152968 2 0.0000 0.9846 0.000 1.000
#> GSM152969 2 0.1633 0.9676 0.024 0.976
#> GSM152970 2 0.8713 0.6042 0.292 0.708
#> GSM152971 2 0.1633 0.9676 0.024 0.976
#> GSM152972 2 0.2603 0.9505 0.044 0.956
#> GSM152973 2 0.0000 0.9846 0.000 1.000
#> GSM152974 2 0.0000 0.9846 0.000 1.000
#> GSM152975 2 0.0000 0.9846 0.000 1.000
#> GSM152976 2 0.2423 0.9542 0.040 0.960
#> GSM152977 2 0.1633 0.9676 0.024 0.976
#> GSM152978 2 0.2236 0.9576 0.036 0.964
#> GSM152979 2 0.0000 0.9846 0.000 1.000
#> GSM152980 2 0.0000 0.9846 0.000 1.000
#> GSM152981 2 0.0000 0.9846 0.000 1.000
#> GSM152982 2 0.0376 0.9821 0.004 0.996
#> GSM152983 2 0.1414 0.9707 0.020 0.980
#> GSM152984 2 0.0000 0.9846 0.000 1.000
#> GSM152985 1 0.0000 0.9838 1.000 0.000
#> GSM152986 2 0.5294 0.8701 0.120 0.880
#> GSM152987 1 0.0000 0.9838 1.000 0.000
#> GSM152988 2 0.0000 0.9846 0.000 1.000
#> GSM152989 1 0.0000 0.9838 1.000 0.000
#> GSM152990 2 0.0000 0.9846 0.000 1.000
#> GSM152991 2 0.0000 0.9846 0.000 1.000
#> GSM187524 1 0.0000 0.9838 1.000 0.000
#> GSM187525 1 0.0000 0.9838 1.000 0.000
#> GSM187526 1 0.0000 0.9838 1.000 0.000
#> GSM187527 1 0.0000 0.9838 1.000 0.000
#> GSM152856 1 0.0000 0.9838 1.000 0.000
#> GSM152857 1 0.0000 0.9838 1.000 0.000
#> GSM152858 1 0.0000 0.9838 1.000 0.000
#> GSM152859 1 0.0000 0.9838 1.000 0.000
#> GSM152860 1 0.0000 0.9838 1.000 0.000
#> GSM152861 1 0.0000 0.9838 1.000 0.000
#> GSM152862 1 0.0000 0.9838 1.000 0.000
#> GSM152863 1 0.0000 0.9838 1.000 0.000
#> GSM152864 1 0.0000 0.9838 1.000 0.000
#> GSM152865 1 0.0000 0.9838 1.000 0.000
#> GSM152866 1 0.0000 0.9838 1.000 0.000
#> GSM152867 1 0.0000 0.9838 1.000 0.000
#> GSM152868 1 0.0000 0.9838 1.000 0.000
#> GSM152869 1 0.0000 0.9838 1.000 0.000
#> GSM152870 1 0.0000 0.9838 1.000 0.000
#> GSM152871 1 0.0000 0.9838 1.000 0.000
#> GSM152872 1 0.0000 0.9838 1.000 0.000
#> GSM152873 1 0.0000 0.9838 1.000 0.000
#> GSM152874 1 0.0000 0.9838 1.000 0.000
#> GSM152875 1 0.0000 0.9838 1.000 0.000
#> GSM152876 1 0.0000 0.9838 1.000 0.000
#> GSM152877 1 0.0000 0.9838 1.000 0.000
#> GSM152878 1 0.0000 0.9838 1.000 0.000
#> GSM152879 1 0.0000 0.9838 1.000 0.000
#> GSM152880 1 0.0000 0.9838 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM152805 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152806 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152807 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM152808 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152809 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM152810 3 0.0983 0.9411 0.004 0.016 0.980
#> GSM152811 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152812 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM152813 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM152814 2 0.2959 0.8851 0.000 0.900 0.100
#> GSM152815 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM152816 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152817 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152818 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152819 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152820 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152821 2 0.3482 0.8648 0.000 0.872 0.128
#> GSM153115 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM153116 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153117 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153118 2 0.5254 0.7065 0.000 0.736 0.264
#> GSM153119 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153120 2 0.0424 0.8909 0.008 0.992 0.000
#> GSM153121 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153122 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153123 2 0.5678 0.6201 0.000 0.684 0.316
#> GSM153124 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM153125 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM153126 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153127 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM153128 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153129 3 0.4346 0.7720 0.000 0.184 0.816
#> GSM153130 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153131 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153132 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153133 2 0.5216 0.7137 0.000 0.740 0.260
#> GSM153134 3 0.1643 0.9340 0.000 0.044 0.956
#> GSM153135 2 0.2448 0.8975 0.000 0.924 0.076
#> GSM153136 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM153137 2 0.1289 0.8993 0.000 0.968 0.032
#> GSM153138 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM153139 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153140 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM153141 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM153142 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153143 2 0.1860 0.8995 0.000 0.948 0.052
#> GSM153144 2 0.3482 0.8661 0.000 0.872 0.128
#> GSM153145 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153146 2 0.4605 0.7876 0.000 0.796 0.204
#> GSM153147 3 0.5497 0.5772 0.000 0.292 0.708
#> GSM153148 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM153149 2 0.6291 0.2180 0.000 0.532 0.468
#> GSM153150 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM153151 2 0.6309 0.1098 0.000 0.504 0.496
#> GSM153152 3 0.1643 0.9343 0.000 0.044 0.956
#> GSM153153 2 0.5760 0.5933 0.000 0.672 0.328
#> GSM153154 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153155 2 0.2625 0.8946 0.000 0.916 0.084
#> GSM153156 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153157 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153158 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153159 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153160 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153161 2 0.2356 0.8983 0.000 0.928 0.072
#> GSM153162 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153163 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153164 3 0.4702 0.7295 0.000 0.212 0.788
#> GSM153165 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153166 3 0.4796 0.7153 0.000 0.220 0.780
#> GSM153167 2 0.6154 0.4106 0.000 0.592 0.408
#> GSM153168 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153169 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153170 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153171 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM153172 2 0.3267 0.8746 0.000 0.884 0.116
#> GSM153173 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM153174 2 0.5859 0.5649 0.000 0.656 0.344
#> GSM153175 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM153176 3 0.6291 0.2107 0.000 0.468 0.532
#> GSM153177 3 0.4750 0.7222 0.000 0.216 0.784
#> GSM152931 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152932 2 0.5905 0.5470 0.000 0.648 0.352
#> GSM152933 3 0.6295 0.0136 0.000 0.472 0.528
#> GSM152934 2 0.0592 0.8983 0.000 0.988 0.012
#> GSM152935 3 0.6126 0.3013 0.000 0.400 0.600
#> GSM152936 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152937 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152938 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152939 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152940 2 0.0747 0.8841 0.016 0.984 0.000
#> GSM152941 1 0.2796 0.9172 0.908 0.092 0.000
#> GSM152942 3 0.1289 0.9422 0.000 0.032 0.968
#> GSM152943 2 0.0237 0.8975 0.000 0.996 0.004
#> GSM152944 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152945 2 0.3038 0.8832 0.000 0.896 0.104
#> GSM152946 2 0.2356 0.8983 0.000 0.928 0.072
#> GSM152947 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152948 2 0.2356 0.8983 0.000 0.928 0.072
#> GSM152949 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152950 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152951 2 0.2356 0.8983 0.000 0.928 0.072
#> GSM152952 2 0.2165 0.8990 0.000 0.936 0.064
#> GSM152953 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM152954 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152955 2 0.5178 0.7069 0.000 0.744 0.256
#> GSM152956 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM152957 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152958 2 0.0747 0.8841 0.016 0.984 0.000
#> GSM152959 2 0.0237 0.8941 0.004 0.996 0.000
#> GSM152960 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152961 2 0.1031 0.8782 0.024 0.976 0.000
#> GSM152962 3 0.1964 0.9240 0.000 0.056 0.944
#> GSM152963 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM152964 3 0.2878 0.8878 0.000 0.096 0.904
#> GSM152965 2 0.3941 0.8397 0.000 0.844 0.156
#> GSM152966 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152967 2 0.2537 0.8966 0.000 0.920 0.080
#> GSM152968 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152969 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152970 2 0.0424 0.8926 0.008 0.992 0.000
#> GSM152971 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152972 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152973 2 0.4750 0.7130 0.000 0.784 0.216
#> GSM152974 2 0.3340 0.8716 0.000 0.880 0.120
#> GSM152975 2 0.2261 0.8989 0.000 0.932 0.068
#> GSM152976 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152977 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152978 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152979 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152980 2 0.2356 0.8986 0.000 0.928 0.072
#> GSM152981 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152982 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152983 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152984 2 0.4750 0.7756 0.000 0.784 0.216
#> GSM152985 2 0.6008 0.3405 0.372 0.628 0.000
#> GSM152986 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152987 1 0.2066 0.9450 0.940 0.060 0.000
#> GSM152988 2 0.0000 0.8969 0.000 1.000 0.000
#> GSM152989 2 0.4702 0.6717 0.212 0.788 0.000
#> GSM152990 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM152991 3 0.1031 0.9498 0.000 0.024 0.976
#> GSM187524 1 0.0424 0.9897 0.992 0.000 0.008
#> GSM187525 1 0.0424 0.9897 0.992 0.000 0.008
#> GSM187526 1 0.0424 0.9897 0.992 0.000 0.008
#> GSM187527 1 0.0424 0.9905 0.992 0.000 0.008
#> GSM152856 1 0.0424 0.9905 0.992 0.000 0.008
#> GSM152857 1 0.0592 0.9885 0.988 0.000 0.012
#> GSM152858 1 0.0747 0.9878 0.984 0.000 0.016
#> GSM152859 1 0.0747 0.9878 0.984 0.000 0.016
#> GSM152860 1 0.0747 0.9878 0.984 0.000 0.016
#> GSM152861 1 0.0000 0.9905 1.000 0.000 0.000
#> GSM152862 1 0.0747 0.9878 0.984 0.000 0.016
#> GSM152863 1 0.0000 0.9905 1.000 0.000 0.000
#> GSM152864 1 0.0000 0.9905 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.9905 1.000 0.000 0.000
#> GSM152866 1 0.0424 0.9905 0.992 0.000 0.008
#> GSM152867 1 0.0000 0.9905 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.9905 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.9905 1.000 0.000 0.000
#> GSM152870 1 0.0747 0.9878 0.984 0.000 0.016
#> GSM152871 1 0.0747 0.9878 0.984 0.000 0.016
#> GSM152872 1 0.0747 0.9878 0.984 0.000 0.016
#> GSM152873 1 0.0424 0.9905 0.992 0.000 0.008
#> GSM152874 1 0.0424 0.9905 0.992 0.000 0.008
#> GSM152875 1 0.0424 0.9905 0.992 0.000 0.008
#> GSM152876 1 0.0424 0.9905 0.992 0.000 0.008
#> GSM152877 1 0.0424 0.9905 0.992 0.000 0.008
#> GSM152878 1 0.0424 0.9905 0.992 0.000 0.008
#> GSM152879 1 0.0424 0.9905 0.992 0.000 0.008
#> GSM152880 1 0.0424 0.9905 0.992 0.000 0.008
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.4456 0.6448 0.000 0.716 0.004 0.280
#> GSM152805 3 0.0469 0.7194 0.000 0.012 0.988 0.000
#> GSM152806 3 0.0469 0.7194 0.000 0.012 0.988 0.000
#> GSM152807 2 0.4999 0.4252 0.000 0.508 0.000 0.492
#> GSM152808 3 0.0469 0.7194 0.000 0.012 0.988 0.000
#> GSM152809 2 0.4999 0.4252 0.000 0.508 0.000 0.492
#> GSM152810 3 0.1940 0.6770 0.000 0.076 0.924 0.000
#> GSM152811 3 0.0469 0.7194 0.000 0.012 0.988 0.000
#> GSM152812 2 0.4999 0.4252 0.000 0.508 0.000 0.492
#> GSM152813 2 0.4360 0.6629 0.000 0.744 0.008 0.248
#> GSM152814 2 0.4262 0.6675 0.000 0.756 0.008 0.236
#> GSM152815 2 0.4999 0.4252 0.000 0.508 0.000 0.492
#> GSM152816 3 0.4697 0.7756 0.000 0.356 0.644 0.000
#> GSM152817 3 0.0469 0.7194 0.000 0.012 0.988 0.000
#> GSM152818 3 0.0469 0.7194 0.000 0.012 0.988 0.000
#> GSM152819 2 0.4543 0.1442 0.000 0.676 0.324 0.000
#> GSM152820 2 0.4790 -0.1833 0.000 0.620 0.380 0.000
#> GSM152821 2 0.4535 0.6673 0.000 0.744 0.016 0.240
#> GSM153115 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM153116 3 0.2530 0.7345 0.000 0.112 0.888 0.000
#> GSM153117 2 0.4522 0.0658 0.000 0.680 0.320 0.000
#> GSM153118 2 0.4562 0.6705 0.000 0.764 0.028 0.208
#> GSM153119 3 0.1474 0.6997 0.000 0.052 0.948 0.000
#> GSM153120 4 0.0188 0.8981 0.000 0.004 0.000 0.996
#> GSM153121 3 0.4713 0.7749 0.000 0.360 0.640 0.000
#> GSM153122 3 0.1557 0.7019 0.000 0.056 0.944 0.000
#> GSM153123 2 0.4234 0.6193 0.000 0.816 0.052 0.132
#> GSM153124 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM153125 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM153126 3 0.4624 0.7837 0.000 0.340 0.660 0.000
#> GSM153127 2 0.4999 0.4252 0.000 0.508 0.000 0.492
#> GSM153128 3 0.4830 0.7658 0.000 0.392 0.608 0.000
#> GSM153129 2 0.4799 0.3484 0.000 0.744 0.224 0.032
#> GSM153130 3 0.4624 0.7837 0.000 0.340 0.660 0.000
#> GSM153131 3 0.4888 0.7101 0.000 0.412 0.588 0.000
#> GSM153132 3 0.4948 0.6658 0.000 0.440 0.560 0.000
#> GSM153133 2 0.4462 0.6340 0.000 0.792 0.044 0.164
#> GSM153134 2 0.4327 0.3549 0.000 0.768 0.216 0.016
#> GSM153135 2 0.4999 0.4252 0.000 0.508 0.000 0.492
#> GSM153136 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM153137 2 0.4999 0.4149 0.000 0.508 0.000 0.492
#> GSM153138 2 0.4996 0.4268 0.000 0.516 0.000 0.484
#> GSM153139 3 0.4624 0.7837 0.000 0.340 0.660 0.000
#> GSM153140 2 0.4961 0.4826 0.000 0.552 0.000 0.448
#> GSM153141 2 0.4999 0.4252 0.000 0.508 0.000 0.492
#> GSM153142 3 0.0592 0.7207 0.000 0.016 0.984 0.000
#> GSM153143 4 0.4992 -0.3579 0.000 0.476 0.000 0.524
#> GSM153144 2 0.3810 0.6595 0.000 0.804 0.008 0.188
#> GSM153145 3 0.0469 0.7194 0.000 0.012 0.988 0.000
#> GSM153146 2 0.4542 0.6713 0.000 0.752 0.020 0.228
#> GSM153147 2 0.5219 0.2868 0.000 0.712 0.244 0.044
#> GSM153148 2 0.4999 0.4252 0.000 0.508 0.000 0.492
#> GSM153149 2 0.4332 0.5978 0.000 0.816 0.072 0.112
#> GSM153150 4 0.0336 0.8959 0.000 0.008 0.000 0.992
#> GSM153151 2 0.5096 0.4555 0.000 0.760 0.156 0.084
#> GSM153152 2 0.4193 0.1961 0.000 0.732 0.268 0.000
#> GSM153153 2 0.4874 0.6531 0.000 0.764 0.056 0.180
#> GSM153154 3 0.4817 0.7415 0.000 0.388 0.612 0.000
#> GSM153155 2 0.4401 0.6501 0.000 0.724 0.004 0.272
#> GSM153156 3 0.4661 0.7790 0.000 0.348 0.652 0.000
#> GSM153157 3 0.0817 0.7228 0.000 0.024 0.976 0.000
#> GSM153158 3 0.4730 0.7647 0.000 0.364 0.636 0.000
#> GSM153159 3 0.2469 0.7431 0.000 0.108 0.892 0.000
#> GSM153160 3 0.4624 0.7837 0.000 0.340 0.660 0.000
#> GSM153161 2 0.4998 0.4253 0.000 0.512 0.000 0.488
#> GSM153162 2 0.4761 -0.1675 0.000 0.628 0.372 0.000
#> GSM153163 3 0.4624 0.7837 0.000 0.340 0.660 0.000
#> GSM153164 2 0.4669 0.4957 0.000 0.780 0.168 0.052
#> GSM153165 3 0.4624 0.7837 0.000 0.340 0.660 0.000
#> GSM153166 2 0.4356 0.4928 0.000 0.804 0.148 0.048
#> GSM153167 2 0.5010 0.5717 0.000 0.772 0.108 0.120
#> GSM153168 3 0.0469 0.7194 0.000 0.012 0.988 0.000
#> GSM153169 3 0.4624 0.7837 0.000 0.340 0.660 0.000
#> GSM153170 3 0.4866 0.7213 0.000 0.404 0.596 0.000
#> GSM153171 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM153172 2 0.4248 0.6723 0.000 0.768 0.012 0.220
#> GSM153173 3 0.4624 0.7837 0.000 0.340 0.660 0.000
#> GSM153174 2 0.5293 0.5853 0.000 0.748 0.100 0.152
#> GSM153175 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM153176 4 0.5714 0.4729 0.000 0.156 0.128 0.716
#> GSM153177 2 0.4387 0.5005 0.000 0.804 0.144 0.052
#> GSM152931 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152932 2 0.4364 0.6192 0.000 0.808 0.056 0.136
#> GSM152933 2 0.5116 0.6037 0.000 0.764 0.108 0.128
#> GSM152934 4 0.1474 0.8606 0.000 0.052 0.000 0.948
#> GSM152935 2 0.5031 0.5157 0.000 0.768 0.140 0.092
#> GSM152936 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152937 3 0.4843 0.7648 0.000 0.396 0.604 0.000
#> GSM152938 3 0.4843 0.7648 0.000 0.396 0.604 0.000
#> GSM152939 4 0.0707 0.8809 0.000 0.020 0.000 0.980
#> GSM152940 4 0.0336 0.8959 0.000 0.008 0.000 0.992
#> GSM152941 1 0.6211 0.5831 0.632 0.072 0.004 0.292
#> GSM152942 3 0.5577 0.7682 0.000 0.328 0.636 0.036
#> GSM152943 4 0.3400 0.6985 0.000 0.180 0.000 0.820
#> GSM152944 3 0.4624 0.7837 0.000 0.340 0.660 0.000
#> GSM152945 2 0.5372 0.4301 0.000 0.544 0.012 0.444
#> GSM152946 2 0.4999 0.4252 0.000 0.508 0.000 0.492
#> GSM152947 4 0.0469 0.8929 0.000 0.012 0.000 0.988
#> GSM152948 2 0.4999 0.4252 0.000 0.508 0.000 0.492
#> GSM152949 3 0.4972 0.6420 0.000 0.456 0.544 0.000
#> GSM152950 3 0.4998 0.5901 0.000 0.488 0.512 0.000
#> GSM152951 2 0.4999 0.4252 0.000 0.508 0.000 0.492
#> GSM152952 2 0.4998 0.4253 0.000 0.512 0.000 0.488
#> GSM152953 2 0.4999 0.4252 0.000 0.508 0.000 0.492
#> GSM152954 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152955 4 0.4931 0.6590 0.000 0.132 0.092 0.776
#> GSM152956 2 0.4999 0.4252 0.000 0.508 0.000 0.492
#> GSM152957 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152958 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152959 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152960 4 0.0188 0.8981 0.000 0.004 0.000 0.996
#> GSM152961 4 0.0188 0.8975 0.004 0.000 0.000 0.996
#> GSM152962 2 0.4933 -0.4696 0.000 0.568 0.432 0.000
#> GSM152963 2 0.4998 0.4253 0.000 0.512 0.000 0.488
#> GSM152964 3 0.3239 0.6469 0.000 0.052 0.880 0.068
#> GSM152965 2 0.4319 0.6633 0.000 0.760 0.012 0.228
#> GSM152966 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152967 2 0.4643 0.5926 0.000 0.656 0.000 0.344
#> GSM152968 3 0.4992 0.5971 0.000 0.476 0.524 0.000
#> GSM152969 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152970 4 0.0188 0.8982 0.000 0.004 0.000 0.996
#> GSM152971 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152972 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152973 4 0.5994 0.2428 0.000 0.296 0.068 0.636
#> GSM152974 2 0.4011 0.6710 0.000 0.784 0.008 0.208
#> GSM152975 4 0.4713 0.0254 0.000 0.360 0.000 0.640
#> GSM152976 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152977 4 0.0188 0.8980 0.000 0.000 0.004 0.996
#> GSM152978 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152979 3 0.4624 0.7837 0.000 0.340 0.660 0.000
#> GSM152980 4 0.4941 -0.2516 0.000 0.436 0.000 0.564
#> GSM152981 3 0.0592 0.7180 0.000 0.016 0.984 0.000
#> GSM152982 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152983 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152984 2 0.7047 0.2551 0.000 0.444 0.120 0.436
#> GSM152985 4 0.3312 0.7655 0.072 0.052 0.000 0.876
#> GSM152986 4 0.0000 0.9002 0.000 0.000 0.000 1.000
#> GSM152987 1 0.5434 0.7778 0.752 0.072 0.012 0.164
#> GSM152988 4 0.1867 0.8150 0.000 0.072 0.000 0.928
#> GSM152989 4 0.1545 0.8536 0.040 0.008 0.000 0.952
#> GSM152990 3 0.4661 0.7790 0.000 0.348 0.652 0.000
#> GSM152991 3 0.4624 0.7420 0.000 0.340 0.660 0.000
#> GSM187524 1 0.2329 0.9353 0.916 0.072 0.012 0.000
#> GSM187525 1 0.2329 0.9353 0.916 0.072 0.012 0.000
#> GSM187526 1 0.2329 0.9353 0.916 0.072 0.012 0.000
#> GSM187527 1 0.1211 0.9503 0.960 0.040 0.000 0.000
#> GSM152856 1 0.1211 0.9503 0.960 0.040 0.000 0.000
#> GSM152857 1 0.1211 0.9503 0.960 0.040 0.000 0.000
#> GSM152858 1 0.2198 0.9408 0.920 0.072 0.008 0.000
#> GSM152859 1 0.2988 0.9254 0.876 0.112 0.012 0.000
#> GSM152860 1 0.2198 0.9408 0.920 0.072 0.008 0.000
#> GSM152861 1 0.0779 0.9514 0.980 0.016 0.004 0.000
#> GSM152862 1 0.2198 0.9408 0.920 0.072 0.008 0.000
#> GSM152863 1 0.0592 0.9517 0.984 0.016 0.000 0.000
#> GSM152864 1 0.0592 0.9517 0.984 0.016 0.000 0.000
#> GSM152865 1 0.0592 0.9517 0.984 0.016 0.000 0.000
#> GSM152866 1 0.1211 0.9503 0.960 0.040 0.000 0.000
#> GSM152867 1 0.0592 0.9517 0.984 0.016 0.000 0.000
#> GSM152868 1 0.0592 0.9517 0.984 0.016 0.000 0.000
#> GSM152869 1 0.0592 0.9517 0.984 0.016 0.000 0.000
#> GSM152870 1 0.2198 0.9408 0.920 0.072 0.008 0.000
#> GSM152871 1 0.2198 0.9408 0.920 0.072 0.008 0.000
#> GSM152872 1 0.2198 0.9408 0.920 0.072 0.008 0.000
#> GSM152873 1 0.1211 0.9503 0.960 0.040 0.000 0.000
#> GSM152874 1 0.1211 0.9503 0.960 0.040 0.000 0.000
#> GSM152875 1 0.1211 0.9503 0.960 0.040 0.000 0.000
#> GSM152876 1 0.1211 0.9503 0.960 0.040 0.000 0.000
#> GSM152877 1 0.1211 0.9503 0.960 0.040 0.000 0.000
#> GSM152878 1 0.1211 0.9503 0.960 0.040 0.000 0.000
#> GSM152879 1 0.1211 0.9503 0.960 0.040 0.000 0.000
#> GSM152880 1 0.1211 0.9503 0.960 0.040 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.4069 0.7965 0.000 0.788 0.136 0.076 0.000
#> GSM152805 5 0.4009 0.9271 0.000 0.004 0.312 0.000 0.684
#> GSM152806 5 0.4009 0.9271 0.000 0.004 0.312 0.000 0.684
#> GSM152807 2 0.3333 0.8047 0.000 0.788 0.004 0.208 0.000
#> GSM152808 5 0.4009 0.9271 0.000 0.004 0.312 0.000 0.684
#> GSM152809 2 0.3333 0.8047 0.000 0.788 0.004 0.208 0.000
#> GSM152810 5 0.4295 0.8848 0.000 0.024 0.248 0.004 0.724
#> GSM152811 5 0.3857 0.9265 0.000 0.000 0.312 0.000 0.688
#> GSM152812 2 0.3333 0.8047 0.000 0.788 0.004 0.208 0.000
#> GSM152813 2 0.3882 0.7826 0.000 0.788 0.168 0.044 0.000
#> GSM152814 2 0.3848 0.7803 0.000 0.788 0.172 0.040 0.000
#> GSM152815 2 0.3333 0.8047 0.000 0.788 0.004 0.208 0.000
#> GSM152816 3 0.1549 0.7748 0.000 0.040 0.944 0.000 0.016
#> GSM152817 5 0.4009 0.9271 0.000 0.004 0.312 0.000 0.684
#> GSM152818 5 0.4009 0.9271 0.000 0.004 0.312 0.000 0.684
#> GSM152819 2 0.4016 0.6798 0.000 0.716 0.272 0.000 0.012
#> GSM152820 2 0.4443 0.2437 0.000 0.524 0.472 0.000 0.004
#> GSM152821 2 0.3914 0.7847 0.000 0.788 0.164 0.048 0.000
#> GSM153115 4 0.0510 0.9462 0.000 0.016 0.000 0.984 0.000
#> GSM153116 5 0.5133 0.7723 0.000 0.044 0.388 0.000 0.568
#> GSM153117 2 0.4126 0.5178 0.000 0.620 0.380 0.000 0.000
#> GSM153118 2 0.3675 0.7703 0.000 0.788 0.188 0.024 0.000
#> GSM153119 5 0.5159 0.8639 0.000 0.072 0.284 0.000 0.644
#> GSM153120 4 0.1582 0.9264 0.000 0.028 0.000 0.944 0.028
#> GSM153121 3 0.1018 0.7817 0.000 0.016 0.968 0.000 0.016
#> GSM153122 5 0.5199 0.8614 0.000 0.072 0.292 0.000 0.636
#> GSM153123 2 0.4470 0.4635 0.000 0.596 0.396 0.004 0.004
#> GSM153124 4 0.0510 0.9462 0.000 0.016 0.000 0.984 0.000
#> GSM153125 4 0.0510 0.9462 0.000 0.016 0.000 0.984 0.000
#> GSM153126 3 0.0693 0.7827 0.000 0.008 0.980 0.000 0.012
#> GSM153127 2 0.3333 0.8047 0.000 0.788 0.004 0.208 0.000
#> GSM153128 3 0.3301 0.6829 0.000 0.080 0.848 0.000 0.072
#> GSM153129 3 0.3661 0.5764 0.000 0.276 0.724 0.000 0.000
#> GSM153130 3 0.0671 0.7776 0.000 0.004 0.980 0.000 0.016
#> GSM153131 3 0.1043 0.7917 0.000 0.040 0.960 0.000 0.000
#> GSM153132 3 0.1478 0.7859 0.000 0.064 0.936 0.000 0.000
#> GSM153133 2 0.4390 0.3792 0.000 0.568 0.428 0.004 0.000
#> GSM153134 3 0.3796 0.5266 0.000 0.300 0.700 0.000 0.000
#> GSM153135 2 0.3333 0.8047 0.000 0.788 0.004 0.208 0.000
#> GSM153136 4 0.0510 0.9462 0.000 0.016 0.000 0.984 0.000
#> GSM153137 2 0.3880 0.7957 0.000 0.772 0.004 0.204 0.020
#> GSM153138 2 0.3718 0.7995 0.000 0.784 0.004 0.196 0.016
#> GSM153139 3 0.0693 0.7827 0.000 0.008 0.980 0.000 0.012
#> GSM153140 2 0.3810 0.8112 0.000 0.788 0.036 0.176 0.000
#> GSM153141 2 0.3333 0.8047 0.000 0.788 0.004 0.208 0.000
#> GSM153142 5 0.4288 0.8610 0.000 0.004 0.384 0.000 0.612
#> GSM153143 2 0.3783 0.7596 0.000 0.740 0.000 0.252 0.008
#> GSM153144 2 0.4299 0.4851 0.000 0.608 0.388 0.004 0.000
#> GSM153145 5 0.4009 0.9271 0.000 0.004 0.312 0.000 0.684
#> GSM153146 2 0.3724 0.7730 0.000 0.788 0.184 0.028 0.000
#> GSM153147 3 0.3612 0.5941 0.000 0.268 0.732 0.000 0.000
#> GSM153148 2 0.3333 0.8047 0.000 0.788 0.004 0.208 0.000
#> GSM153149 2 0.3579 0.7274 0.000 0.756 0.240 0.004 0.000
#> GSM153150 4 0.1195 0.9370 0.000 0.028 0.000 0.960 0.012
#> GSM153151 3 0.5596 0.3641 0.000 0.376 0.552 0.004 0.068
#> GSM153152 3 0.3636 0.5860 0.000 0.272 0.728 0.000 0.000
#> GSM153153 2 0.3675 0.7703 0.000 0.788 0.188 0.024 0.000
#> GSM153154 3 0.1121 0.7910 0.000 0.044 0.956 0.000 0.000
#> GSM153155 2 0.4054 0.7957 0.000 0.788 0.140 0.072 0.000
#> GSM153156 3 0.0693 0.7860 0.000 0.008 0.980 0.000 0.012
#> GSM153157 5 0.4565 0.8257 0.000 0.012 0.408 0.000 0.580
#> GSM153158 3 0.0794 0.7909 0.000 0.028 0.972 0.000 0.000
#> GSM153159 3 0.3582 0.3214 0.000 0.008 0.768 0.000 0.224
#> GSM153160 3 0.0693 0.7827 0.000 0.008 0.980 0.000 0.012
#> GSM153161 2 0.3611 0.8013 0.000 0.780 0.004 0.208 0.008
#> GSM153162 3 0.3003 0.6989 0.000 0.188 0.812 0.000 0.000
#> GSM153163 3 0.0693 0.7827 0.000 0.008 0.980 0.000 0.012
#> GSM153164 2 0.3826 0.7307 0.000 0.752 0.236 0.008 0.004
#> GSM153165 3 0.0693 0.7827 0.000 0.008 0.980 0.000 0.012
#> GSM153166 2 0.3684 0.6776 0.000 0.720 0.280 0.000 0.000
#> GSM153167 3 0.4182 0.3882 0.000 0.352 0.644 0.004 0.000
#> GSM153168 5 0.3837 0.9259 0.000 0.000 0.308 0.000 0.692
#> GSM153169 3 0.0693 0.7827 0.000 0.008 0.980 0.000 0.012
#> GSM153170 3 0.0963 0.7920 0.000 0.036 0.964 0.000 0.000
#> GSM153171 4 0.0404 0.9463 0.000 0.012 0.000 0.988 0.000
#> GSM153172 2 0.3621 0.7671 0.000 0.788 0.192 0.020 0.000
#> GSM153173 3 0.0693 0.7827 0.000 0.008 0.980 0.000 0.012
#> GSM153174 3 0.3906 0.5372 0.000 0.292 0.704 0.004 0.000
#> GSM153175 4 0.0566 0.9458 0.000 0.012 0.004 0.984 0.000
#> GSM153176 4 0.3003 0.7237 0.000 0.000 0.188 0.812 0.000
#> GSM153177 2 0.3480 0.7162 0.000 0.752 0.248 0.000 0.000
#> GSM152931 4 0.0510 0.9462 0.000 0.016 0.000 0.984 0.000
#> GSM152932 2 0.3741 0.7015 0.000 0.732 0.264 0.004 0.000
#> GSM152933 2 0.3710 0.7673 0.000 0.784 0.192 0.024 0.000
#> GSM152934 4 0.3702 0.8300 0.000 0.080 0.008 0.832 0.080
#> GSM152935 2 0.5776 0.5407 0.000 0.624 0.280 0.024 0.072
#> GSM152936 4 0.0865 0.9447 0.000 0.024 0.000 0.972 0.004
#> GSM152937 3 0.3748 0.6609 0.000 0.092 0.824 0.004 0.080
#> GSM152938 3 0.3119 0.7021 0.000 0.072 0.860 0.000 0.068
#> GSM152939 4 0.0912 0.9381 0.000 0.012 0.016 0.972 0.000
#> GSM152940 4 0.1403 0.9218 0.000 0.024 0.000 0.952 0.024
#> GSM152941 4 0.7771 0.0108 0.328 0.088 0.008 0.440 0.136
#> GSM152942 3 0.0798 0.7854 0.000 0.008 0.976 0.016 0.000
#> GSM152943 4 0.5278 0.6527 0.000 0.216 0.012 0.688 0.084
#> GSM152944 3 0.0693 0.7827 0.000 0.008 0.980 0.000 0.012
#> GSM152945 2 0.4883 0.7144 0.000 0.752 0.020 0.128 0.100
#> GSM152946 2 0.3874 0.7992 0.000 0.776 0.008 0.200 0.016
#> GSM152947 4 0.1211 0.9256 0.000 0.024 0.000 0.960 0.016
#> GSM152948 2 0.3333 0.8047 0.000 0.788 0.004 0.208 0.000
#> GSM152949 3 0.1478 0.7859 0.000 0.064 0.936 0.000 0.000
#> GSM152950 3 0.2077 0.7754 0.000 0.084 0.908 0.000 0.008
#> GSM152951 2 0.3333 0.8047 0.000 0.788 0.004 0.208 0.000
#> GSM152952 2 0.3719 0.7995 0.000 0.776 0.004 0.208 0.012
#> GSM152953 2 0.3300 0.8050 0.000 0.792 0.004 0.204 0.000
#> GSM152954 4 0.0566 0.9462 0.000 0.012 0.000 0.984 0.004
#> GSM152955 4 0.5789 0.6774 0.000 0.160 0.048 0.688 0.104
#> GSM152956 2 0.3333 0.8047 0.000 0.788 0.004 0.208 0.000
#> GSM152957 4 0.0290 0.9453 0.000 0.008 0.000 0.992 0.000
#> GSM152958 4 0.0324 0.9441 0.000 0.004 0.000 0.992 0.004
#> GSM152959 4 0.0451 0.9437 0.000 0.004 0.000 0.988 0.008
#> GSM152960 4 0.1117 0.9418 0.000 0.016 0.000 0.964 0.020
#> GSM152961 4 0.0324 0.9441 0.000 0.004 0.000 0.992 0.004
#> GSM152962 3 0.3966 0.7049 0.000 0.132 0.796 0.000 0.072
#> GSM152963 2 0.3333 0.8047 0.000 0.788 0.004 0.208 0.000
#> GSM152964 5 0.6173 0.7800 0.000 0.084 0.216 0.060 0.640
#> GSM152965 2 0.3992 0.7678 0.000 0.812 0.128 0.032 0.028
#> GSM152966 4 0.0510 0.9462 0.000 0.016 0.000 0.984 0.000
#> GSM152967 2 0.4171 0.8043 0.000 0.784 0.104 0.112 0.000
#> GSM152968 3 0.1671 0.7804 0.000 0.076 0.924 0.000 0.000
#> GSM152969 4 0.0671 0.9458 0.000 0.016 0.000 0.980 0.004
#> GSM152970 4 0.0451 0.9421 0.004 0.008 0.000 0.988 0.000
#> GSM152971 4 0.0510 0.9462 0.000 0.016 0.000 0.984 0.000
#> GSM152972 4 0.0510 0.9462 0.000 0.016 0.000 0.984 0.000
#> GSM152973 3 0.4147 0.4674 0.000 0.008 0.676 0.316 0.000
#> GSM152974 2 0.3521 0.7357 0.000 0.764 0.232 0.004 0.000
#> GSM152975 2 0.4310 0.5417 0.000 0.604 0.004 0.392 0.000
#> GSM152976 4 0.0404 0.9463 0.000 0.012 0.000 0.988 0.000
#> GSM152977 4 0.0693 0.9440 0.000 0.008 0.000 0.980 0.012
#> GSM152978 4 0.0807 0.9451 0.000 0.012 0.000 0.976 0.012
#> GSM152979 3 0.0290 0.7856 0.000 0.008 0.992 0.000 0.000
#> GSM152980 2 0.4375 0.5916 0.000 0.628 0.004 0.364 0.004
#> GSM152981 5 0.4067 0.9216 0.000 0.008 0.300 0.000 0.692
#> GSM152982 4 0.0510 0.9462 0.000 0.016 0.000 0.984 0.000
#> GSM152983 4 0.0510 0.9462 0.000 0.016 0.000 0.984 0.000
#> GSM152984 3 0.4297 0.5689 0.000 0.036 0.728 0.236 0.000
#> GSM152985 4 0.1087 0.9278 0.008 0.008 0.000 0.968 0.016
#> GSM152986 4 0.0404 0.9463 0.000 0.012 0.000 0.988 0.000
#> GSM152987 1 0.7810 0.5011 0.492 0.104 0.008 0.236 0.160
#> GSM152988 4 0.1670 0.9073 0.000 0.012 0.052 0.936 0.000
#> GSM152989 4 0.0613 0.9396 0.008 0.004 0.000 0.984 0.004
#> GSM152990 3 0.0290 0.7856 0.000 0.008 0.992 0.000 0.000
#> GSM152991 3 0.6498 -0.2776 0.000 0.200 0.460 0.000 0.340
#> GSM187524 1 0.4779 0.8168 0.760 0.084 0.008 0.008 0.140
#> GSM187525 1 0.4779 0.8168 0.760 0.084 0.008 0.008 0.140
#> GSM187526 1 0.4779 0.8168 0.760 0.084 0.008 0.008 0.140
#> GSM187527 1 0.2079 0.9010 0.916 0.020 0.000 0.000 0.064
#> GSM152856 1 0.2171 0.9004 0.912 0.024 0.000 0.000 0.064
#> GSM152857 1 0.2171 0.9004 0.912 0.024 0.000 0.000 0.064
#> GSM152858 1 0.3002 0.8830 0.876 0.048 0.000 0.008 0.068
#> GSM152859 1 0.4887 0.8123 0.744 0.092 0.008 0.004 0.152
#> GSM152860 1 0.3002 0.8830 0.876 0.048 0.000 0.008 0.068
#> GSM152861 1 0.1095 0.9035 0.968 0.012 0.000 0.008 0.012
#> GSM152862 1 0.3002 0.8830 0.876 0.048 0.000 0.008 0.068
#> GSM152863 1 0.0579 0.9054 0.984 0.008 0.000 0.008 0.000
#> GSM152864 1 0.0579 0.9054 0.984 0.008 0.000 0.008 0.000
#> GSM152865 1 0.0579 0.9054 0.984 0.008 0.000 0.008 0.000
#> GSM152866 1 0.2236 0.8998 0.908 0.024 0.000 0.000 0.068
#> GSM152867 1 0.0579 0.9054 0.984 0.008 0.000 0.008 0.000
#> GSM152868 1 0.0579 0.9054 0.984 0.008 0.000 0.008 0.000
#> GSM152869 1 0.0579 0.9054 0.984 0.008 0.000 0.008 0.000
#> GSM152870 1 0.3002 0.8830 0.876 0.048 0.000 0.008 0.068
#> GSM152871 1 0.3002 0.8830 0.876 0.048 0.000 0.008 0.068
#> GSM152872 1 0.3002 0.8830 0.876 0.048 0.000 0.008 0.068
#> GSM152873 1 0.2171 0.9004 0.912 0.024 0.000 0.000 0.064
#> GSM152874 1 0.2171 0.9004 0.912 0.024 0.000 0.000 0.064
#> GSM152875 1 0.2171 0.9004 0.912 0.024 0.000 0.000 0.064
#> GSM152876 1 0.2171 0.9004 0.912 0.024 0.000 0.000 0.064
#> GSM152877 1 0.2171 0.9004 0.912 0.024 0.000 0.000 0.064
#> GSM152878 1 0.2171 0.9004 0.912 0.024 0.000 0.000 0.064
#> GSM152879 1 0.2171 0.9004 0.912 0.024 0.000 0.000 0.064
#> GSM152880 1 0.2171 0.9004 0.912 0.024 0.000 0.000 0.064
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.2862 0.7895 0.000 0.864 0.080 0.048 0.000 0.008
#> GSM152805 5 0.2879 0.8573 0.000 0.004 0.176 0.000 0.816 0.004
#> GSM152806 5 0.2879 0.8573 0.000 0.004 0.176 0.000 0.816 0.004
#> GSM152807 2 0.2362 0.7839 0.000 0.860 0.000 0.136 0.000 0.004
#> GSM152808 5 0.2738 0.8567 0.000 0.004 0.176 0.000 0.820 0.000
#> GSM152809 2 0.2362 0.7839 0.000 0.860 0.000 0.136 0.000 0.004
#> GSM152810 5 0.3616 0.7461 0.000 0.000 0.076 0.000 0.792 0.132
#> GSM152811 5 0.2597 0.8567 0.000 0.000 0.176 0.000 0.824 0.000
#> GSM152812 2 0.2219 0.7845 0.000 0.864 0.000 0.136 0.000 0.000
#> GSM152813 2 0.2653 0.7847 0.000 0.868 0.100 0.028 0.000 0.004
#> GSM152814 2 0.2404 0.7797 0.000 0.872 0.112 0.016 0.000 0.000
#> GSM152815 2 0.2219 0.7845 0.000 0.864 0.000 0.136 0.000 0.000
#> GSM152816 3 0.2265 0.7917 0.000 0.068 0.900 0.000 0.008 0.024
#> GSM152817 5 0.2738 0.8567 0.000 0.004 0.176 0.000 0.820 0.000
#> GSM152818 5 0.2879 0.8573 0.000 0.004 0.176 0.000 0.816 0.004
#> GSM152819 2 0.3868 0.7162 0.000 0.772 0.172 0.000 0.012 0.044
#> GSM152820 2 0.4696 0.4457 0.000 0.600 0.352 0.000 0.008 0.040
#> GSM152821 2 0.2798 0.7807 0.000 0.860 0.108 0.020 0.000 0.012
#> GSM153115 4 0.0291 0.9321 0.000 0.004 0.000 0.992 0.000 0.004
#> GSM153116 5 0.6477 0.5001 0.000 0.052 0.216 0.000 0.512 0.220
#> GSM153117 2 0.4617 0.4926 0.000 0.624 0.324 0.000 0.004 0.048
#> GSM153118 2 0.3057 0.7710 0.000 0.844 0.120 0.008 0.004 0.024
#> GSM153119 5 0.5353 0.4802 0.000 0.000 0.116 0.000 0.516 0.368
#> GSM153120 4 0.2420 0.8356 0.000 0.004 0.000 0.864 0.004 0.128
#> GSM153121 3 0.1411 0.8155 0.000 0.004 0.936 0.000 0.000 0.060
#> GSM153122 5 0.5609 0.4558 0.000 0.004 0.132 0.000 0.496 0.368
#> GSM153123 2 0.4624 0.2576 0.000 0.528 0.432 0.000 0.000 0.040
#> GSM153124 4 0.0291 0.9321 0.000 0.004 0.000 0.992 0.000 0.004
#> GSM153125 4 0.0291 0.9321 0.000 0.004 0.000 0.992 0.000 0.004
#> GSM153126 3 0.0767 0.8226 0.000 0.008 0.976 0.000 0.004 0.012
#> GSM153127 2 0.2219 0.7845 0.000 0.864 0.000 0.136 0.000 0.000
#> GSM153128 3 0.4494 0.1770 0.000 0.012 0.512 0.000 0.012 0.464
#> GSM153129 3 0.3088 0.7189 0.000 0.172 0.808 0.000 0.000 0.020
#> GSM153130 3 0.0520 0.8245 0.000 0.008 0.984 0.000 0.008 0.000
#> GSM153131 3 0.2069 0.8174 0.000 0.068 0.908 0.000 0.004 0.020
#> GSM153132 3 0.2653 0.8054 0.000 0.064 0.876 0.000 0.004 0.056
#> GSM153133 2 0.5029 0.3151 0.000 0.544 0.376 0.000 0.000 0.080
#> GSM153134 3 0.3212 0.7043 0.000 0.180 0.800 0.000 0.004 0.016
#> GSM153135 2 0.2473 0.7826 0.000 0.856 0.000 0.136 0.000 0.008
#> GSM153136 4 0.0551 0.9329 0.000 0.004 0.000 0.984 0.004 0.008
#> GSM153137 2 0.3264 0.7569 0.000 0.820 0.004 0.136 0.000 0.040
#> GSM153138 2 0.3579 0.7524 0.000 0.804 0.000 0.120 0.004 0.072
#> GSM153139 3 0.0405 0.8266 0.000 0.008 0.988 0.000 0.004 0.000
#> GSM153140 2 0.3306 0.7908 0.000 0.840 0.032 0.104 0.004 0.020
#> GSM153141 2 0.2362 0.7840 0.000 0.860 0.000 0.136 0.004 0.000
#> GSM153142 5 0.4313 0.7439 0.000 0.000 0.284 0.000 0.668 0.048
#> GSM153143 2 0.3588 0.7484 0.000 0.788 0.000 0.152 0.000 0.060
#> GSM153144 2 0.4326 0.3523 0.000 0.572 0.404 0.000 0.000 0.024
#> GSM153145 5 0.2879 0.8573 0.000 0.004 0.176 0.000 0.816 0.004
#> GSM153146 2 0.3031 0.7747 0.000 0.848 0.116 0.012 0.004 0.020
#> GSM153147 3 0.2968 0.7288 0.000 0.168 0.816 0.000 0.000 0.016
#> GSM153148 2 0.2219 0.7845 0.000 0.864 0.000 0.136 0.000 0.000
#> GSM153149 2 0.3202 0.7457 0.000 0.816 0.144 0.000 0.000 0.040
#> GSM153150 4 0.1493 0.9051 0.000 0.004 0.000 0.936 0.004 0.056
#> GSM153151 6 0.5744 -0.0240 0.000 0.168 0.408 0.000 0.000 0.424
#> GSM153152 3 0.3923 0.6674 0.000 0.192 0.748 0.000 0.000 0.060
#> GSM153153 2 0.3135 0.7696 0.000 0.840 0.120 0.008 0.004 0.028
#> GSM153154 3 0.1856 0.8217 0.000 0.048 0.920 0.000 0.000 0.032
#> GSM153155 2 0.3198 0.7844 0.000 0.844 0.100 0.032 0.000 0.024
#> GSM153156 3 0.0806 0.8278 0.000 0.008 0.972 0.000 0.000 0.020
#> GSM153157 5 0.4569 0.7108 0.000 0.000 0.304 0.000 0.636 0.060
#> GSM153158 3 0.2452 0.8107 0.000 0.044 0.892 0.000 0.008 0.056
#> GSM153159 3 0.3727 0.5384 0.000 0.004 0.768 0.000 0.188 0.040
#> GSM153160 3 0.0767 0.8226 0.000 0.008 0.976 0.000 0.004 0.012
#> GSM153161 2 0.2572 0.7809 0.000 0.852 0.000 0.136 0.000 0.012
#> GSM153162 3 0.2214 0.7996 0.000 0.096 0.888 0.000 0.000 0.016
#> GSM153163 3 0.0405 0.8266 0.000 0.008 0.988 0.000 0.004 0.000
#> GSM153164 2 0.3706 0.7382 0.000 0.792 0.156 0.004 0.008 0.040
#> GSM153165 3 0.0405 0.8266 0.000 0.008 0.988 0.000 0.004 0.000
#> GSM153166 2 0.3770 0.6849 0.000 0.752 0.212 0.000 0.004 0.032
#> GSM153167 3 0.3758 0.6151 0.000 0.232 0.740 0.000 0.004 0.024
#> GSM153168 5 0.2597 0.8567 0.000 0.000 0.176 0.000 0.824 0.000
#> GSM153169 3 0.0665 0.8243 0.000 0.008 0.980 0.000 0.008 0.004
#> GSM153170 3 0.1007 0.8284 0.000 0.044 0.956 0.000 0.000 0.000
#> GSM153171 4 0.0291 0.9333 0.000 0.004 0.000 0.992 0.000 0.004
#> GSM153172 2 0.2680 0.7698 0.000 0.856 0.124 0.004 0.000 0.016
#> GSM153173 3 0.0405 0.8266 0.000 0.008 0.988 0.000 0.004 0.000
#> GSM153174 3 0.3202 0.7133 0.000 0.176 0.800 0.000 0.000 0.024
#> GSM153175 4 0.0291 0.9321 0.000 0.004 0.000 0.992 0.000 0.004
#> GSM153176 4 0.2914 0.7034 0.000 0.004 0.152 0.832 0.004 0.008
#> GSM153177 2 0.3388 0.7392 0.000 0.804 0.156 0.000 0.004 0.036
#> GSM152931 4 0.0291 0.9321 0.000 0.004 0.000 0.992 0.000 0.004
#> GSM152932 2 0.3580 0.7052 0.000 0.772 0.196 0.000 0.004 0.028
#> GSM152933 2 0.3100 0.7685 0.000 0.840 0.124 0.008 0.004 0.024
#> GSM152934 4 0.4313 -0.0194 0.000 0.004 0.012 0.504 0.000 0.480
#> GSM152935 6 0.5812 0.3178 0.000 0.348 0.192 0.000 0.000 0.460
#> GSM152936 4 0.1155 0.9222 0.000 0.004 0.000 0.956 0.004 0.036
#> GSM152937 3 0.4500 0.0970 0.000 0.012 0.496 0.000 0.012 0.480
#> GSM152938 3 0.3955 0.4773 0.000 0.012 0.668 0.000 0.004 0.316
#> GSM152939 4 0.0976 0.9178 0.000 0.008 0.008 0.968 0.000 0.016
#> GSM152940 4 0.2056 0.8786 0.000 0.012 0.000 0.904 0.004 0.080
#> GSM152941 4 0.8009 0.0742 0.224 0.072 0.000 0.420 0.108 0.176
#> GSM152942 3 0.1325 0.8225 0.000 0.012 0.956 0.016 0.004 0.012
#> GSM152943 6 0.5583 0.1669 0.000 0.108 0.008 0.428 0.000 0.456
#> GSM152944 3 0.0405 0.8266 0.000 0.008 0.988 0.000 0.004 0.000
#> GSM152945 6 0.5254 0.2370 0.000 0.404 0.012 0.056 0.004 0.524
#> GSM152946 2 0.3672 0.7454 0.000 0.792 0.004 0.140 0.000 0.064
#> GSM152947 4 0.2068 0.8819 0.000 0.008 0.000 0.904 0.008 0.080
#> GSM152948 2 0.2362 0.7839 0.000 0.860 0.000 0.136 0.000 0.004
#> GSM152949 3 0.1719 0.8227 0.000 0.060 0.924 0.000 0.000 0.016
#> GSM152950 3 0.2801 0.8001 0.000 0.072 0.860 0.000 0.000 0.068
#> GSM152951 2 0.2664 0.7803 0.000 0.848 0.000 0.136 0.000 0.016
#> GSM152952 2 0.2664 0.7792 0.000 0.848 0.000 0.136 0.000 0.016
#> GSM152953 2 0.2504 0.7830 0.000 0.856 0.000 0.136 0.004 0.004
#> GSM152954 4 0.0291 0.9324 0.000 0.000 0.000 0.992 0.004 0.004
#> GSM152955 6 0.5672 0.2167 0.000 0.068 0.016 0.412 0.012 0.492
#> GSM152956 2 0.2219 0.7845 0.000 0.864 0.000 0.136 0.000 0.000
#> GSM152957 4 0.0146 0.9326 0.000 0.004 0.000 0.996 0.000 0.000
#> GSM152958 4 0.0551 0.9324 0.000 0.004 0.000 0.984 0.004 0.008
#> GSM152959 4 0.0291 0.9324 0.000 0.000 0.000 0.992 0.004 0.004
#> GSM152960 4 0.1003 0.9221 0.000 0.004 0.000 0.964 0.004 0.028
#> GSM152961 4 0.0767 0.9269 0.000 0.012 0.000 0.976 0.004 0.008
#> GSM152962 3 0.4731 0.2055 0.000 0.048 0.524 0.000 0.000 0.428
#> GSM152963 2 0.2362 0.7832 0.000 0.860 0.000 0.136 0.000 0.004
#> GSM152964 6 0.5672 -0.2600 0.000 0.000 0.056 0.048 0.380 0.516
#> GSM152965 2 0.4862 0.4233 0.000 0.632 0.052 0.016 0.000 0.300
#> GSM152966 4 0.0291 0.9321 0.000 0.004 0.000 0.992 0.000 0.004
#> GSM152967 2 0.3666 0.7854 0.000 0.824 0.068 0.060 0.000 0.048
#> GSM152968 3 0.1951 0.8168 0.000 0.076 0.908 0.000 0.000 0.016
#> GSM152969 4 0.0146 0.9326 0.000 0.004 0.000 0.996 0.000 0.000
#> GSM152970 4 0.0551 0.9318 0.000 0.004 0.000 0.984 0.008 0.004
#> GSM152971 4 0.0405 0.9329 0.000 0.004 0.000 0.988 0.000 0.008
#> GSM152972 4 0.0291 0.9329 0.000 0.004 0.000 0.992 0.004 0.000
#> GSM152973 3 0.3462 0.6495 0.000 0.008 0.792 0.180 0.004 0.016
#> GSM152974 2 0.3457 0.7506 0.000 0.808 0.136 0.004 0.000 0.052
#> GSM152975 2 0.4470 0.4351 0.000 0.604 0.000 0.356 0.000 0.040
#> GSM152976 4 0.0551 0.9325 0.000 0.004 0.000 0.984 0.004 0.008
#> GSM152977 4 0.0508 0.9318 0.000 0.000 0.000 0.984 0.004 0.012
#> GSM152978 4 0.0508 0.9311 0.000 0.000 0.000 0.984 0.004 0.012
#> GSM152979 3 0.0260 0.8273 0.000 0.008 0.992 0.000 0.000 0.000
#> GSM152980 2 0.4323 0.5258 0.000 0.652 0.000 0.312 0.004 0.032
#> GSM152981 5 0.3213 0.8432 0.000 0.000 0.160 0.000 0.808 0.032
#> GSM152982 4 0.0551 0.9325 0.000 0.004 0.000 0.984 0.004 0.008
#> GSM152983 4 0.0551 0.9325 0.000 0.004 0.000 0.984 0.004 0.008
#> GSM152984 3 0.3644 0.6912 0.000 0.032 0.804 0.144 0.004 0.016
#> GSM152985 4 0.1173 0.9213 0.000 0.016 0.000 0.960 0.008 0.016
#> GSM152986 4 0.0436 0.9329 0.000 0.004 0.000 0.988 0.004 0.004
#> GSM152987 1 0.8167 0.2937 0.364 0.076 0.000 0.172 0.108 0.280
#> GSM152988 4 0.1850 0.8628 0.000 0.008 0.052 0.924 0.000 0.016
#> GSM152989 4 0.0665 0.9291 0.000 0.008 0.000 0.980 0.004 0.008
#> GSM152990 3 0.0458 0.8291 0.000 0.016 0.984 0.000 0.000 0.000
#> GSM152991 6 0.7604 -0.0261 0.000 0.168 0.240 0.000 0.284 0.308
#> GSM187524 1 0.6156 0.6400 0.592 0.068 0.000 0.004 0.124 0.212
#> GSM187525 1 0.6156 0.6400 0.592 0.068 0.000 0.004 0.124 0.212
#> GSM187526 1 0.6156 0.6400 0.592 0.068 0.000 0.004 0.124 0.212
#> GSM187527 1 0.3542 0.7920 0.800 0.016 0.000 0.000 0.028 0.156
#> GSM152856 1 0.3542 0.7920 0.800 0.016 0.000 0.000 0.028 0.156
#> GSM152857 1 0.3542 0.7920 0.800 0.016 0.000 0.000 0.028 0.156
#> GSM152858 1 0.4333 0.7392 0.740 0.036 0.000 0.000 0.036 0.188
#> GSM152859 1 0.6194 0.6255 0.560 0.076 0.000 0.000 0.108 0.256
#> GSM152860 1 0.4333 0.7392 0.740 0.036 0.000 0.000 0.036 0.188
#> GSM152861 1 0.1578 0.7939 0.936 0.012 0.000 0.000 0.004 0.048
#> GSM152862 1 0.4333 0.7392 0.740 0.036 0.000 0.000 0.036 0.188
#> GSM152863 1 0.0436 0.8022 0.988 0.004 0.000 0.000 0.004 0.004
#> GSM152864 1 0.0436 0.8022 0.988 0.004 0.000 0.000 0.004 0.004
#> GSM152865 1 0.0436 0.8022 0.988 0.004 0.000 0.000 0.004 0.004
#> GSM152866 1 0.3578 0.7909 0.796 0.016 0.000 0.000 0.028 0.160
#> GSM152867 1 0.0436 0.8022 0.988 0.004 0.000 0.000 0.004 0.004
#> GSM152868 1 0.0436 0.8022 0.988 0.004 0.000 0.000 0.004 0.004
#> GSM152869 1 0.0436 0.8022 0.988 0.004 0.000 0.000 0.004 0.004
#> GSM152870 1 0.4333 0.7392 0.740 0.036 0.000 0.000 0.036 0.188
#> GSM152871 1 0.4333 0.7392 0.740 0.036 0.000 0.000 0.036 0.188
#> GSM152872 1 0.4333 0.7392 0.740 0.036 0.000 0.000 0.036 0.188
#> GSM152873 1 0.3542 0.7920 0.800 0.016 0.000 0.000 0.028 0.156
#> GSM152874 1 0.3542 0.7920 0.800 0.016 0.000 0.000 0.028 0.156
#> GSM152875 1 0.3542 0.7920 0.800 0.016 0.000 0.000 0.028 0.156
#> GSM152876 1 0.3542 0.7920 0.800 0.016 0.000 0.000 0.028 0.156
#> GSM152877 1 0.3542 0.7920 0.800 0.016 0.000 0.000 0.028 0.156
#> GSM152878 1 0.3542 0.7920 0.800 0.016 0.000 0.000 0.028 0.156
#> GSM152879 1 0.3542 0.7920 0.800 0.016 0.000 0.000 0.028 0.156
#> GSM152880 1 0.3542 0.7920 0.800 0.016 0.000 0.000 0.028 0.156
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> MAD:kmeans 169 4.70e-26 2
#> MAD:kmeans 164 8.27e-29 3
#> MAD:kmeans 133 1.48e-24 4
#> MAD:kmeans 161 3.73e-32 5
#> MAD:kmeans 148 2.88e-32 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "skmeans"]
# you can also extract it by
# res = res_list["MAD:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.975 0.990 0.4839 0.518 0.518
#> 3 3 0.827 0.864 0.940 0.3802 0.794 0.611
#> 4 4 0.811 0.832 0.911 0.1117 0.916 0.751
#> 5 5 0.723 0.690 0.815 0.0704 0.905 0.654
#> 6 6 0.716 0.624 0.786 0.0395 0.977 0.889
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.9883 0.000 1.000
#> GSM152805 2 0.0000 0.9883 0.000 1.000
#> GSM152806 2 0.0000 0.9883 0.000 1.000
#> GSM152807 2 0.0000 0.9883 0.000 1.000
#> GSM152808 2 0.0000 0.9883 0.000 1.000
#> GSM152809 2 0.0000 0.9883 0.000 1.000
#> GSM152810 1 0.0376 0.9887 0.996 0.004
#> GSM152811 2 0.0000 0.9883 0.000 1.000
#> GSM152812 2 0.0000 0.9883 0.000 1.000
#> GSM152813 2 0.0000 0.9883 0.000 1.000
#> GSM152814 2 0.0000 0.9883 0.000 1.000
#> GSM152815 2 0.0000 0.9883 0.000 1.000
#> GSM152816 2 0.0000 0.9883 0.000 1.000
#> GSM152817 2 0.0000 0.9883 0.000 1.000
#> GSM152818 2 0.0000 0.9883 0.000 1.000
#> GSM152819 2 0.0000 0.9883 0.000 1.000
#> GSM152820 2 0.0000 0.9883 0.000 1.000
#> GSM152821 2 0.0000 0.9883 0.000 1.000
#> GSM153115 1 0.0000 0.9922 1.000 0.000
#> GSM153116 2 0.0000 0.9883 0.000 1.000
#> GSM153117 2 0.0000 0.9883 0.000 1.000
#> GSM153118 2 0.0000 0.9883 0.000 1.000
#> GSM153119 2 0.0000 0.9883 0.000 1.000
#> GSM153120 1 0.0000 0.9922 1.000 0.000
#> GSM153121 2 0.0000 0.9883 0.000 1.000
#> GSM153122 2 0.0000 0.9883 0.000 1.000
#> GSM153123 2 0.0000 0.9883 0.000 1.000
#> GSM153124 2 0.9993 0.0676 0.484 0.516
#> GSM153125 1 0.0000 0.9922 1.000 0.000
#> GSM153126 2 0.0000 0.9883 0.000 1.000
#> GSM153127 2 0.0000 0.9883 0.000 1.000
#> GSM153128 2 0.0000 0.9883 0.000 1.000
#> GSM153129 2 0.0000 0.9883 0.000 1.000
#> GSM153130 2 0.0000 0.9883 0.000 1.000
#> GSM153131 2 0.0000 0.9883 0.000 1.000
#> GSM153132 2 0.0000 0.9883 0.000 1.000
#> GSM153133 2 0.0000 0.9883 0.000 1.000
#> GSM153134 2 0.0000 0.9883 0.000 1.000
#> GSM153135 2 0.0000 0.9883 0.000 1.000
#> GSM153136 1 0.0000 0.9922 1.000 0.000
#> GSM153137 1 0.8661 0.5938 0.712 0.288
#> GSM153138 2 0.0000 0.9883 0.000 1.000
#> GSM153139 2 0.0000 0.9883 0.000 1.000
#> GSM153140 2 0.0000 0.9883 0.000 1.000
#> GSM153141 2 0.0000 0.9883 0.000 1.000
#> GSM153142 2 0.0000 0.9883 0.000 1.000
#> GSM153143 2 0.0000 0.9883 0.000 1.000
#> GSM153144 2 0.0000 0.9883 0.000 1.000
#> GSM153145 2 0.0000 0.9883 0.000 1.000
#> GSM153146 2 0.0000 0.9883 0.000 1.000
#> GSM153147 2 0.0000 0.9883 0.000 1.000
#> GSM153148 2 0.0000 0.9883 0.000 1.000
#> GSM153149 2 0.0000 0.9883 0.000 1.000
#> GSM153150 1 0.0000 0.9922 1.000 0.000
#> GSM153151 2 0.0000 0.9883 0.000 1.000
#> GSM153152 2 0.0000 0.9883 0.000 1.000
#> GSM153153 2 0.0000 0.9883 0.000 1.000
#> GSM153154 2 0.0000 0.9883 0.000 1.000
#> GSM153155 2 0.0000 0.9883 0.000 1.000
#> GSM153156 2 0.0000 0.9883 0.000 1.000
#> GSM153157 2 0.0000 0.9883 0.000 1.000
#> GSM153158 2 0.0000 0.9883 0.000 1.000
#> GSM153159 2 0.0000 0.9883 0.000 1.000
#> GSM153160 2 0.0000 0.9883 0.000 1.000
#> GSM153161 2 0.0000 0.9883 0.000 1.000
#> GSM153162 2 0.0000 0.9883 0.000 1.000
#> GSM153163 2 0.0000 0.9883 0.000 1.000
#> GSM153164 2 0.0000 0.9883 0.000 1.000
#> GSM153165 2 0.0000 0.9883 0.000 1.000
#> GSM153166 2 0.0000 0.9883 0.000 1.000
#> GSM153167 2 0.0000 0.9883 0.000 1.000
#> GSM153168 2 0.0000 0.9883 0.000 1.000
#> GSM153169 2 0.0000 0.9883 0.000 1.000
#> GSM153170 2 0.0000 0.9883 0.000 1.000
#> GSM153171 1 0.0000 0.9922 1.000 0.000
#> GSM153172 2 0.0000 0.9883 0.000 1.000
#> GSM153173 2 0.0000 0.9883 0.000 1.000
#> GSM153174 2 0.0000 0.9883 0.000 1.000
#> GSM153175 1 0.0000 0.9922 1.000 0.000
#> GSM153176 1 0.0000 0.9922 1.000 0.000
#> GSM153177 2 0.0000 0.9883 0.000 1.000
#> GSM152931 1 0.0000 0.9922 1.000 0.000
#> GSM152932 2 0.0000 0.9883 0.000 1.000
#> GSM152933 2 0.0000 0.9883 0.000 1.000
#> GSM152934 1 0.4298 0.9020 0.912 0.088
#> GSM152935 2 0.0000 0.9883 0.000 1.000
#> GSM152936 1 0.0000 0.9922 1.000 0.000
#> GSM152937 2 0.0000 0.9883 0.000 1.000
#> GSM152938 2 0.0000 0.9883 0.000 1.000
#> GSM152939 1 0.0376 0.9886 0.996 0.004
#> GSM152940 1 0.0000 0.9922 1.000 0.000
#> GSM152941 1 0.0000 0.9922 1.000 0.000
#> GSM152942 2 0.0000 0.9883 0.000 1.000
#> GSM152943 1 0.3733 0.9203 0.928 0.072
#> GSM152944 2 0.0000 0.9883 0.000 1.000
#> GSM152945 2 0.0000 0.9883 0.000 1.000
#> GSM152946 2 0.0000 0.9883 0.000 1.000
#> GSM152947 1 0.0000 0.9922 1.000 0.000
#> GSM152948 2 0.0000 0.9883 0.000 1.000
#> GSM152949 2 0.0000 0.9883 0.000 1.000
#> GSM152950 2 0.0000 0.9883 0.000 1.000
#> GSM152951 2 0.0000 0.9883 0.000 1.000
#> GSM152952 2 0.0000 0.9883 0.000 1.000
#> GSM152953 2 0.0000 0.9883 0.000 1.000
#> GSM152954 1 0.0000 0.9922 1.000 0.000
#> GSM152955 2 0.0376 0.9845 0.004 0.996
#> GSM152956 2 0.0000 0.9883 0.000 1.000
#> GSM152957 1 0.0000 0.9922 1.000 0.000
#> GSM152958 1 0.0000 0.9922 1.000 0.000
#> GSM152959 1 0.0000 0.9922 1.000 0.000
#> GSM152960 1 0.0000 0.9922 1.000 0.000
#> GSM152961 1 0.0000 0.9922 1.000 0.000
#> GSM152962 2 0.0000 0.9883 0.000 1.000
#> GSM152963 2 0.0000 0.9883 0.000 1.000
#> GSM152964 2 0.8909 0.5543 0.308 0.692
#> GSM152965 2 0.0000 0.9883 0.000 1.000
#> GSM152966 1 0.0000 0.9922 1.000 0.000
#> GSM152967 2 0.0000 0.9883 0.000 1.000
#> GSM152968 2 0.0000 0.9883 0.000 1.000
#> GSM152969 1 0.0000 0.9922 1.000 0.000
#> GSM152970 1 0.0000 0.9922 1.000 0.000
#> GSM152971 1 0.0000 0.9922 1.000 0.000
#> GSM152972 1 0.0000 0.9922 1.000 0.000
#> GSM152973 2 0.9580 0.3903 0.380 0.620
#> GSM152974 2 0.0000 0.9883 0.000 1.000
#> GSM152975 2 0.0376 0.9845 0.004 0.996
#> GSM152976 1 0.0000 0.9922 1.000 0.000
#> GSM152977 1 0.0000 0.9922 1.000 0.000
#> GSM152978 1 0.0000 0.9922 1.000 0.000
#> GSM152979 2 0.0000 0.9883 0.000 1.000
#> GSM152980 2 0.0000 0.9883 0.000 1.000
#> GSM152981 2 0.0000 0.9883 0.000 1.000
#> GSM152982 1 0.0000 0.9922 1.000 0.000
#> GSM152983 1 0.0000 0.9922 1.000 0.000
#> GSM152984 2 0.0000 0.9883 0.000 1.000
#> GSM152985 1 0.0000 0.9922 1.000 0.000
#> GSM152986 1 0.0000 0.9922 1.000 0.000
#> GSM152987 1 0.0000 0.9922 1.000 0.000
#> GSM152988 1 0.3274 0.9330 0.940 0.060
#> GSM152989 1 0.0000 0.9922 1.000 0.000
#> GSM152990 2 0.0000 0.9883 0.000 1.000
#> GSM152991 2 0.0000 0.9883 0.000 1.000
#> GSM187524 1 0.0000 0.9922 1.000 0.000
#> GSM187525 1 0.0000 0.9922 1.000 0.000
#> GSM187526 1 0.0000 0.9922 1.000 0.000
#> GSM187527 1 0.0000 0.9922 1.000 0.000
#> GSM152856 1 0.0000 0.9922 1.000 0.000
#> GSM152857 1 0.0000 0.9922 1.000 0.000
#> GSM152858 1 0.0000 0.9922 1.000 0.000
#> GSM152859 1 0.0000 0.9922 1.000 0.000
#> GSM152860 1 0.0000 0.9922 1.000 0.000
#> GSM152861 1 0.0000 0.9922 1.000 0.000
#> GSM152862 1 0.0000 0.9922 1.000 0.000
#> GSM152863 1 0.0000 0.9922 1.000 0.000
#> GSM152864 1 0.0000 0.9922 1.000 0.000
#> GSM152865 1 0.0000 0.9922 1.000 0.000
#> GSM152866 1 0.0000 0.9922 1.000 0.000
#> GSM152867 1 0.0000 0.9922 1.000 0.000
#> GSM152868 1 0.0000 0.9922 1.000 0.000
#> GSM152869 1 0.0000 0.9922 1.000 0.000
#> GSM152870 1 0.0000 0.9922 1.000 0.000
#> GSM152871 1 0.0000 0.9922 1.000 0.000
#> GSM152872 1 0.0000 0.9922 1.000 0.000
#> GSM152873 1 0.0000 0.9922 1.000 0.000
#> GSM152874 1 0.0000 0.9922 1.000 0.000
#> GSM152875 1 0.0000 0.9922 1.000 0.000
#> GSM152876 1 0.0000 0.9922 1.000 0.000
#> GSM152877 1 0.0000 0.9922 1.000 0.000
#> GSM152878 1 0.0000 0.9922 1.000 0.000
#> GSM152879 1 0.0000 0.9922 1.000 0.000
#> GSM152880 1 0.0000 0.9922 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152805 3 0.0000 0.953 0.000 0.000 1.000
#> GSM152806 3 0.0000 0.953 0.000 0.000 1.000
#> GSM152807 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152808 3 0.0000 0.953 0.000 0.000 1.000
#> GSM152809 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152810 3 0.2878 0.863 0.096 0.000 0.904
#> GSM152811 3 0.0000 0.953 0.000 0.000 1.000
#> GSM152812 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152813 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152814 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152815 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152816 3 0.1031 0.938 0.000 0.024 0.976
#> GSM152817 3 0.0000 0.953 0.000 0.000 1.000
#> GSM152818 3 0.0000 0.953 0.000 0.000 1.000
#> GSM152819 2 0.6252 0.234 0.000 0.556 0.444
#> GSM152820 3 0.3686 0.825 0.000 0.140 0.860
#> GSM152821 2 0.0000 0.919 0.000 1.000 0.000
#> GSM153115 1 0.4062 0.806 0.836 0.164 0.000
#> GSM153116 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153117 3 0.6260 0.118 0.000 0.448 0.552
#> GSM153118 2 0.1529 0.900 0.000 0.960 0.040
#> GSM153119 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153120 1 0.0592 0.930 0.988 0.012 0.000
#> GSM153121 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153122 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153123 2 0.3482 0.834 0.000 0.872 0.128
#> GSM153124 2 0.5098 0.618 0.248 0.752 0.000
#> GSM153125 1 0.6309 0.109 0.504 0.496 0.000
#> GSM153126 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153127 2 0.0000 0.919 0.000 1.000 0.000
#> GSM153128 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153129 3 0.5138 0.662 0.000 0.252 0.748
#> GSM153130 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153131 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153132 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153133 2 0.4399 0.763 0.000 0.812 0.188
#> GSM153134 2 0.6168 0.357 0.000 0.588 0.412
#> GSM153135 2 0.0000 0.919 0.000 1.000 0.000
#> GSM153136 1 0.1163 0.922 0.972 0.028 0.000
#> GSM153137 2 0.0000 0.919 0.000 1.000 0.000
#> GSM153138 2 0.0237 0.917 0.000 0.996 0.004
#> GSM153139 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153140 2 0.0000 0.919 0.000 1.000 0.000
#> GSM153141 2 0.0000 0.919 0.000 1.000 0.000
#> GSM153142 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153143 2 0.0000 0.919 0.000 1.000 0.000
#> GSM153144 2 0.0000 0.919 0.000 1.000 0.000
#> GSM153145 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153146 2 0.0000 0.919 0.000 1.000 0.000
#> GSM153147 3 0.3192 0.862 0.000 0.112 0.888
#> GSM153148 2 0.0000 0.919 0.000 1.000 0.000
#> GSM153149 2 0.2066 0.888 0.000 0.940 0.060
#> GSM153150 1 0.0237 0.934 0.996 0.004 0.000
#> GSM153151 3 0.4062 0.794 0.000 0.164 0.836
#> GSM153152 3 0.6079 0.338 0.000 0.388 0.612
#> GSM153153 2 0.0424 0.916 0.000 0.992 0.008
#> GSM153154 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153155 2 0.0237 0.918 0.000 0.996 0.004
#> GSM153156 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153157 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153158 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153159 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153160 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153161 2 0.0000 0.919 0.000 1.000 0.000
#> GSM153162 3 0.2959 0.871 0.000 0.100 0.900
#> GSM153163 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153164 2 0.4842 0.716 0.000 0.776 0.224
#> GSM153165 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153166 2 0.2537 0.874 0.000 0.920 0.080
#> GSM153167 2 0.5968 0.469 0.000 0.636 0.364
#> GSM153168 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153169 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153170 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153171 1 0.0892 0.926 0.980 0.020 0.000
#> GSM153172 2 0.0000 0.919 0.000 1.000 0.000
#> GSM153173 3 0.0000 0.953 0.000 0.000 1.000
#> GSM153174 2 0.6204 0.309 0.000 0.576 0.424
#> GSM153175 1 0.3267 0.854 0.884 0.116 0.000
#> GSM153176 1 0.6274 0.172 0.544 0.000 0.456
#> GSM153177 2 0.2711 0.869 0.000 0.912 0.088
#> GSM152931 1 0.5650 0.593 0.688 0.312 0.000
#> GSM152932 2 0.2356 0.881 0.000 0.928 0.072
#> GSM152933 2 0.2878 0.861 0.000 0.904 0.096
#> GSM152934 1 0.9198 0.370 0.532 0.200 0.268
#> GSM152935 3 0.5650 0.537 0.000 0.312 0.688
#> GSM152936 1 0.3038 0.867 0.896 0.104 0.000
#> GSM152937 3 0.0000 0.953 0.000 0.000 1.000
#> GSM152938 3 0.0000 0.953 0.000 0.000 1.000
#> GSM152939 1 0.6553 0.356 0.580 0.412 0.008
#> GSM152940 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152941 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152942 3 0.0000 0.953 0.000 0.000 1.000
#> GSM152943 2 0.6104 0.418 0.348 0.648 0.004
#> GSM152944 3 0.0000 0.953 0.000 0.000 1.000
#> GSM152945 2 0.6111 0.386 0.000 0.604 0.396
#> GSM152946 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152947 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152948 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152949 3 0.0237 0.951 0.000 0.004 0.996
#> GSM152950 3 0.0424 0.948 0.000 0.008 0.992
#> GSM152951 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152952 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152953 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152954 1 0.0237 0.934 0.996 0.004 0.000
#> GSM152955 3 0.3340 0.848 0.000 0.120 0.880
#> GSM152956 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152957 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152958 1 0.0424 0.932 0.992 0.008 0.000
#> GSM152959 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152960 1 0.3116 0.860 0.892 0.108 0.000
#> GSM152961 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152962 3 0.0747 0.943 0.000 0.016 0.984
#> GSM152963 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152964 3 0.0237 0.950 0.004 0.000 0.996
#> GSM152965 2 0.1643 0.899 0.000 0.956 0.044
#> GSM152966 1 0.5327 0.659 0.728 0.272 0.000
#> GSM152967 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152968 3 0.0237 0.951 0.000 0.004 0.996
#> GSM152969 1 0.4291 0.788 0.820 0.180 0.000
#> GSM152970 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152971 1 0.3879 0.819 0.848 0.152 0.000
#> GSM152972 1 0.2356 0.892 0.928 0.072 0.000
#> GSM152973 3 0.3148 0.893 0.036 0.048 0.916
#> GSM152974 2 0.0000 0.919 0.000 1.000 0.000
#> GSM152975 2 0.2590 0.881 0.004 0.924 0.072
#> GSM152976 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152977 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152978 1 0.2356 0.893 0.928 0.072 0.000
#> GSM152979 3 0.0000 0.953 0.000 0.000 1.000
#> GSM152980 2 0.0237 0.917 0.000 0.996 0.004
#> GSM152981 3 0.0000 0.953 0.000 0.000 1.000
#> GSM152982 1 0.3148 0.889 0.916 0.048 0.036
#> GSM152983 1 0.0747 0.928 0.984 0.016 0.000
#> GSM152984 3 0.2066 0.910 0.000 0.060 0.940
#> GSM152985 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152986 1 0.0424 0.932 0.992 0.008 0.000
#> GSM152987 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152988 1 0.9335 0.147 0.456 0.376 0.168
#> GSM152989 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152990 3 0.0000 0.953 0.000 0.000 1.000
#> GSM152991 3 0.1529 0.925 0.000 0.040 0.960
#> GSM187524 1 0.0000 0.936 1.000 0.000 0.000
#> GSM187525 1 0.0000 0.936 1.000 0.000 0.000
#> GSM187526 1 0.0000 0.936 1.000 0.000 0.000
#> GSM187527 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152856 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152857 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152858 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152859 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152860 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152861 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152862 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152863 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152864 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152866 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152867 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152870 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152871 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152873 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152874 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152875 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152876 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152877 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152878 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152879 1 0.0000 0.936 1.000 0.000 0.000
#> GSM152880 1 0.0000 0.936 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.0188 0.8951 0.000 0.996 0.000 0.004
#> GSM152805 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM152806 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM152807 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM152808 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM152809 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM152810 3 0.4720 0.5052 0.324 0.000 0.672 0.004
#> GSM152811 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM152812 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM152813 2 0.0000 0.8948 0.000 1.000 0.000 0.000
#> GSM152814 2 0.0188 0.8945 0.000 0.996 0.000 0.004
#> GSM152815 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM152816 3 0.1256 0.9071 0.000 0.028 0.964 0.008
#> GSM152817 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM152818 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM152819 2 0.5105 0.2736 0.000 0.564 0.432 0.004
#> GSM152820 3 0.3751 0.7344 0.000 0.196 0.800 0.004
#> GSM152821 2 0.0188 0.8951 0.000 0.996 0.004 0.000
#> GSM153115 4 0.1706 0.8722 0.036 0.016 0.000 0.948
#> GSM153116 3 0.0524 0.9146 0.000 0.008 0.988 0.004
#> GSM153117 3 0.5404 0.0396 0.000 0.476 0.512 0.012
#> GSM153118 2 0.0336 0.8948 0.000 0.992 0.008 0.000
#> GSM153119 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM153120 4 0.5500 0.2875 0.464 0.016 0.000 0.520
#> GSM153121 3 0.1545 0.9102 0.000 0.008 0.952 0.040
#> GSM153122 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM153123 2 0.2775 0.8467 0.000 0.896 0.084 0.020
#> GSM153124 4 0.2310 0.8403 0.008 0.068 0.004 0.920
#> GSM153125 4 0.1624 0.8662 0.020 0.028 0.000 0.952
#> GSM153126 3 0.1722 0.9074 0.000 0.008 0.944 0.048
#> GSM153127 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM153128 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM153129 3 0.5337 0.6373 0.000 0.260 0.696 0.044
#> GSM153130 3 0.0779 0.9149 0.000 0.004 0.980 0.016
#> GSM153131 3 0.1520 0.9133 0.000 0.020 0.956 0.024
#> GSM153132 3 0.0804 0.9156 0.000 0.008 0.980 0.012
#> GSM153133 2 0.4511 0.7366 0.000 0.784 0.176 0.040
#> GSM153134 2 0.5666 0.4285 0.000 0.616 0.348 0.036
#> GSM153135 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM153136 4 0.1661 0.8732 0.052 0.004 0.000 0.944
#> GSM153137 2 0.0469 0.8940 0.000 0.988 0.000 0.012
#> GSM153138 2 0.0657 0.8937 0.000 0.984 0.004 0.012
#> GSM153139 3 0.0927 0.9147 0.000 0.008 0.976 0.016
#> GSM153140 2 0.0817 0.8898 0.000 0.976 0.000 0.024
#> GSM153141 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM153142 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM153143 2 0.2589 0.8233 0.000 0.884 0.000 0.116
#> GSM153144 2 0.1489 0.8819 0.000 0.952 0.004 0.044
#> GSM153145 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM153146 2 0.0000 0.8948 0.000 1.000 0.000 0.000
#> GSM153147 3 0.4756 0.7602 0.000 0.176 0.772 0.052
#> GSM153148 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM153149 2 0.1256 0.8874 0.000 0.964 0.028 0.008
#> GSM153150 4 0.3649 0.7873 0.204 0.000 0.000 0.796
#> GSM153151 3 0.4797 0.6506 0.000 0.260 0.720 0.020
#> GSM153152 3 0.6163 0.2318 0.000 0.416 0.532 0.052
#> GSM153153 2 0.0188 0.8945 0.000 0.996 0.000 0.004
#> GSM153154 3 0.1388 0.9137 0.000 0.012 0.960 0.028
#> GSM153155 2 0.0524 0.8940 0.000 0.988 0.008 0.004
#> GSM153156 3 0.1004 0.9144 0.000 0.004 0.972 0.024
#> GSM153157 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM153158 3 0.1297 0.9140 0.000 0.020 0.964 0.016
#> GSM153159 3 0.0524 0.9146 0.000 0.004 0.988 0.008
#> GSM153160 3 0.1452 0.9117 0.000 0.008 0.956 0.036
#> GSM153161 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM153162 3 0.4337 0.8009 0.000 0.140 0.808 0.052
#> GSM153163 3 0.1042 0.9147 0.000 0.008 0.972 0.020
#> GSM153164 2 0.4194 0.7022 0.000 0.764 0.228 0.008
#> GSM153165 3 0.1452 0.9115 0.000 0.008 0.956 0.036
#> GSM153166 2 0.2861 0.8406 0.000 0.888 0.096 0.016
#> GSM153167 2 0.5855 0.3941 0.000 0.600 0.356 0.044
#> GSM153168 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM153169 3 0.0188 0.9144 0.000 0.000 0.996 0.004
#> GSM153170 3 0.1452 0.9115 0.000 0.008 0.956 0.036
#> GSM153171 4 0.1743 0.8729 0.056 0.004 0.000 0.940
#> GSM153172 2 0.0336 0.8938 0.000 0.992 0.000 0.008
#> GSM153173 3 0.1356 0.9123 0.000 0.008 0.960 0.032
#> GSM153174 2 0.6228 0.3391 0.000 0.572 0.364 0.064
#> GSM153175 4 0.0469 0.8625 0.012 0.000 0.000 0.988
#> GSM153176 4 0.5496 0.6376 0.064 0.000 0.232 0.704
#> GSM153177 2 0.2675 0.8439 0.000 0.892 0.100 0.008
#> GSM152931 4 0.1411 0.8674 0.020 0.020 0.000 0.960
#> GSM152932 2 0.2413 0.8625 0.000 0.916 0.064 0.020
#> GSM152933 2 0.1716 0.8703 0.000 0.936 0.064 0.000
#> GSM152934 4 0.7734 0.6251 0.140 0.104 0.132 0.624
#> GSM152935 3 0.4999 0.5171 0.000 0.328 0.660 0.012
#> GSM152936 4 0.1970 0.8734 0.060 0.008 0.000 0.932
#> GSM152937 3 0.0657 0.9149 0.000 0.004 0.984 0.012
#> GSM152938 3 0.1256 0.9131 0.000 0.008 0.964 0.028
#> GSM152939 4 0.0376 0.8542 0.000 0.004 0.004 0.992
#> GSM152940 4 0.4072 0.7349 0.252 0.000 0.000 0.748
#> GSM152941 1 0.0336 0.9641 0.992 0.000 0.000 0.008
#> GSM152942 3 0.2480 0.8873 0.000 0.008 0.904 0.088
#> GSM152943 2 0.7203 0.0900 0.124 0.488 0.004 0.384
#> GSM152944 3 0.1042 0.9145 0.000 0.008 0.972 0.020
#> GSM152945 2 0.5966 0.5660 0.000 0.648 0.280 0.072
#> GSM152946 2 0.1978 0.8703 0.000 0.928 0.004 0.068
#> GSM152947 4 0.4605 0.6103 0.336 0.000 0.000 0.664
#> GSM152948 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM152949 3 0.1938 0.9051 0.000 0.012 0.936 0.052
#> GSM152950 3 0.2761 0.8901 0.000 0.048 0.904 0.048
#> GSM152951 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM152952 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM152953 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM152954 4 0.1557 0.8720 0.056 0.000 0.000 0.944
#> GSM152955 3 0.5473 0.6529 0.000 0.084 0.724 0.192
#> GSM152956 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM152957 4 0.3400 0.8080 0.180 0.000 0.000 0.820
#> GSM152958 4 0.2149 0.8643 0.088 0.000 0.000 0.912
#> GSM152959 4 0.4855 0.4805 0.400 0.000 0.000 0.600
#> GSM152960 4 0.5332 0.7554 0.184 0.080 0.000 0.736
#> GSM152961 4 0.2216 0.8626 0.092 0.000 0.000 0.908
#> GSM152962 3 0.2699 0.8850 0.000 0.068 0.904 0.028
#> GSM152963 2 0.0336 0.8953 0.000 0.992 0.000 0.008
#> GSM152964 3 0.1284 0.8997 0.012 0.000 0.964 0.024
#> GSM152965 2 0.1677 0.8837 0.000 0.948 0.040 0.012
#> GSM152966 4 0.1388 0.8705 0.028 0.012 0.000 0.960
#> GSM152967 2 0.1716 0.8771 0.000 0.936 0.000 0.064
#> GSM152968 3 0.2675 0.8920 0.000 0.044 0.908 0.048
#> GSM152969 4 0.1584 0.8726 0.036 0.012 0.000 0.952
#> GSM152970 1 0.4746 0.2945 0.632 0.000 0.000 0.368
#> GSM152971 4 0.1356 0.8715 0.032 0.008 0.000 0.960
#> GSM152972 4 0.1635 0.8732 0.044 0.008 0.000 0.948
#> GSM152973 4 0.5018 0.3911 0.000 0.012 0.332 0.656
#> GSM152974 2 0.0469 0.8939 0.000 0.988 0.000 0.012
#> GSM152975 2 0.6446 0.4146 0.000 0.584 0.088 0.328
#> GSM152976 4 0.2814 0.8435 0.132 0.000 0.000 0.868
#> GSM152977 4 0.2197 0.8700 0.048 0.000 0.024 0.928
#> GSM152978 4 0.3731 0.8396 0.120 0.036 0.000 0.844
#> GSM152979 3 0.1151 0.9139 0.000 0.008 0.968 0.024
#> GSM152980 2 0.4844 0.5490 0.000 0.688 0.012 0.300
#> GSM152981 3 0.0188 0.9135 0.000 0.000 0.996 0.004
#> GSM152982 4 0.0469 0.8626 0.012 0.000 0.000 0.988
#> GSM152983 4 0.1474 0.8726 0.052 0.000 0.000 0.948
#> GSM152984 3 0.5736 0.5332 0.000 0.044 0.628 0.328
#> GSM152985 4 0.4877 0.4657 0.408 0.000 0.000 0.592
#> GSM152986 4 0.1557 0.8720 0.056 0.000 0.000 0.944
#> GSM152987 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152988 4 0.0657 0.8510 0.000 0.012 0.004 0.984
#> GSM152989 1 0.4746 0.2805 0.632 0.000 0.000 0.368
#> GSM152990 3 0.1452 0.9115 0.000 0.008 0.956 0.036
#> GSM152991 3 0.1398 0.9006 0.000 0.040 0.956 0.004
#> GSM187524 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM187525 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM187526 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM187527 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152856 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152857 1 0.0188 0.9677 0.996 0.000 0.000 0.004
#> GSM152858 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152859 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152860 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152861 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152862 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152863 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152864 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152866 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152867 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152868 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152870 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152871 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152872 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152873 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152875 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152876 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152877 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152878 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152879 1 0.0000 0.9726 1.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.9726 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.2179 0.8337 0.000 0.888 0.112 0.000 0.000
#> GSM152805 5 0.1270 0.7094 0.000 0.000 0.052 0.000 0.948
#> GSM152806 5 0.0794 0.7179 0.000 0.000 0.028 0.000 0.972
#> GSM152807 2 0.0703 0.8517 0.000 0.976 0.024 0.000 0.000
#> GSM152808 5 0.0880 0.7176 0.000 0.000 0.032 0.000 0.968
#> GSM152809 2 0.0609 0.8519 0.000 0.980 0.020 0.000 0.000
#> GSM152810 5 0.2419 0.6583 0.064 0.000 0.028 0.004 0.904
#> GSM152811 5 0.0771 0.7182 0.000 0.000 0.020 0.004 0.976
#> GSM152812 2 0.0290 0.8516 0.000 0.992 0.008 0.000 0.000
#> GSM152813 2 0.1197 0.8501 0.000 0.952 0.048 0.000 0.000
#> GSM152814 2 0.1410 0.8472 0.000 0.940 0.060 0.000 0.000
#> GSM152815 2 0.0162 0.8510 0.000 0.996 0.004 0.000 0.000
#> GSM152816 5 0.4747 0.1359 0.000 0.028 0.352 0.000 0.620
#> GSM152817 5 0.0880 0.7176 0.000 0.000 0.032 0.000 0.968
#> GSM152818 5 0.0880 0.7176 0.000 0.000 0.032 0.000 0.968
#> GSM152819 5 0.5776 0.3609 0.000 0.288 0.124 0.000 0.588
#> GSM152820 5 0.5167 0.4548 0.000 0.092 0.240 0.000 0.668
#> GSM152821 2 0.0963 0.8520 0.000 0.964 0.036 0.000 0.000
#> GSM153115 4 0.0865 0.8481 0.000 0.004 0.024 0.972 0.000
#> GSM153116 5 0.2144 0.7019 0.000 0.020 0.068 0.000 0.912
#> GSM153117 5 0.6800 -0.0134 0.000 0.320 0.304 0.000 0.376
#> GSM153118 2 0.2046 0.8411 0.000 0.916 0.068 0.000 0.016
#> GSM153119 5 0.0880 0.7151 0.000 0.000 0.032 0.000 0.968
#> GSM153120 4 0.6459 0.4681 0.332 0.036 0.080 0.548 0.004
#> GSM153121 3 0.3837 0.6648 0.000 0.000 0.692 0.000 0.308
#> GSM153122 5 0.1671 0.6965 0.000 0.000 0.076 0.000 0.924
#> GSM153123 3 0.4787 0.0303 0.000 0.432 0.548 0.000 0.020
#> GSM153124 4 0.3479 0.7966 0.000 0.080 0.084 0.836 0.000
#> GSM153125 4 0.0955 0.8492 0.000 0.004 0.028 0.968 0.000
#> GSM153126 3 0.3949 0.6532 0.000 0.000 0.668 0.000 0.332
#> GSM153127 2 0.0290 0.8509 0.000 0.992 0.008 0.000 0.000
#> GSM153128 5 0.3395 0.5859 0.000 0.000 0.236 0.000 0.764
#> GSM153129 3 0.4496 0.6394 0.000 0.092 0.752 0.000 0.156
#> GSM153130 3 0.4268 0.5441 0.000 0.000 0.556 0.000 0.444
#> GSM153131 3 0.4641 0.4134 0.000 0.012 0.532 0.000 0.456
#> GSM153132 3 0.4743 0.2993 0.000 0.016 0.512 0.000 0.472
#> GSM153133 3 0.4658 -0.1019 0.000 0.484 0.504 0.000 0.012
#> GSM153134 3 0.4757 0.5474 0.000 0.204 0.716 0.000 0.080
#> GSM153135 2 0.0404 0.8509 0.000 0.988 0.012 0.000 0.000
#> GSM153136 4 0.0727 0.8496 0.004 0.004 0.012 0.980 0.000
#> GSM153137 2 0.1682 0.8403 0.000 0.940 0.044 0.012 0.004
#> GSM153138 2 0.2748 0.8288 0.000 0.880 0.096 0.008 0.016
#> GSM153139 3 0.4210 0.5840 0.000 0.000 0.588 0.000 0.412
#> GSM153140 2 0.3035 0.8235 0.000 0.856 0.112 0.032 0.000
#> GSM153141 2 0.0290 0.8514 0.000 0.992 0.008 0.000 0.000
#> GSM153142 5 0.2074 0.6652 0.000 0.000 0.104 0.000 0.896
#> GSM153143 2 0.3572 0.7957 0.000 0.840 0.064 0.088 0.008
#> GSM153144 3 0.4294 -0.0824 0.000 0.468 0.532 0.000 0.000
#> GSM153145 5 0.0880 0.7176 0.000 0.000 0.032 0.000 0.968
#> GSM153146 2 0.1430 0.8511 0.000 0.944 0.052 0.000 0.004
#> GSM153147 3 0.3991 0.6577 0.000 0.048 0.792 0.004 0.156
#> GSM153148 2 0.0290 0.8513 0.000 0.992 0.008 0.000 0.000
#> GSM153149 2 0.4924 0.6063 0.000 0.668 0.272 0.000 0.060
#> GSM153150 4 0.4268 0.7835 0.132 0.016 0.060 0.792 0.000
#> GSM153151 3 0.6184 0.3560 0.000 0.160 0.560 0.004 0.276
#> GSM153152 3 0.5142 0.5067 0.000 0.244 0.668 0.000 0.088
#> GSM153153 2 0.1965 0.8343 0.000 0.904 0.096 0.000 0.000
#> GSM153154 3 0.4238 0.5928 0.000 0.004 0.628 0.000 0.368
#> GSM153155 2 0.2352 0.8382 0.000 0.896 0.092 0.008 0.004
#> GSM153156 3 0.4138 0.6111 0.000 0.000 0.616 0.000 0.384
#> GSM153157 5 0.1205 0.7146 0.000 0.000 0.040 0.004 0.956
#> GSM153158 5 0.4787 0.1368 0.000 0.028 0.364 0.000 0.608
#> GSM153159 5 0.3752 0.3026 0.000 0.000 0.292 0.000 0.708
#> GSM153160 3 0.4030 0.6444 0.000 0.000 0.648 0.000 0.352
#> GSM153161 2 0.0703 0.8511 0.000 0.976 0.024 0.000 0.000
#> GSM153162 3 0.3805 0.6660 0.000 0.032 0.784 0.000 0.184
#> GSM153163 3 0.4297 0.4873 0.000 0.000 0.528 0.000 0.472
#> GSM153164 2 0.6445 0.1051 0.000 0.456 0.184 0.000 0.360
#> GSM153165 3 0.3895 0.6630 0.000 0.000 0.680 0.000 0.320
#> GSM153166 2 0.5167 0.2979 0.000 0.552 0.404 0.000 0.044
#> GSM153167 3 0.4612 0.5534 0.000 0.180 0.736 0.000 0.084
#> GSM153168 5 0.0771 0.7182 0.000 0.000 0.020 0.004 0.976
#> GSM153169 5 0.4297 -0.3797 0.000 0.000 0.472 0.000 0.528
#> GSM153170 3 0.3906 0.6709 0.000 0.004 0.704 0.000 0.292
#> GSM153171 4 0.1365 0.8499 0.004 0.004 0.040 0.952 0.000
#> GSM153172 2 0.1410 0.8454 0.000 0.940 0.060 0.000 0.000
#> GSM153173 3 0.4015 0.6507 0.000 0.000 0.652 0.000 0.348
#> GSM153174 3 0.3983 0.5707 0.000 0.164 0.784 0.000 0.052
#> GSM153175 4 0.1478 0.8398 0.000 0.000 0.064 0.936 0.000
#> GSM153176 4 0.6729 0.4943 0.052 0.000 0.212 0.584 0.152
#> GSM153177 2 0.5037 0.4698 0.000 0.616 0.336 0.000 0.048
#> GSM152931 4 0.0955 0.8490 0.000 0.004 0.028 0.968 0.000
#> GSM152932 2 0.4637 0.2994 0.000 0.536 0.452 0.000 0.012
#> GSM152933 2 0.2871 0.8216 0.000 0.872 0.088 0.000 0.040
#> GSM152934 4 0.8685 0.3084 0.072 0.064 0.260 0.412 0.192
#> GSM152935 5 0.6758 0.1105 0.000 0.304 0.292 0.000 0.404
#> GSM152936 4 0.1779 0.8490 0.008 0.004 0.040 0.940 0.008
#> GSM152937 5 0.4449 -0.0347 0.000 0.000 0.484 0.004 0.512
#> GSM152938 3 0.4166 0.6005 0.000 0.004 0.648 0.000 0.348
#> GSM152939 4 0.2561 0.7996 0.000 0.000 0.144 0.856 0.000
#> GSM152940 4 0.4269 0.7508 0.176 0.004 0.044 0.772 0.004
#> GSM152941 1 0.1469 0.9294 0.948 0.000 0.016 0.036 0.000
#> GSM152942 3 0.4397 0.6604 0.000 0.000 0.696 0.028 0.276
#> GSM152943 2 0.8635 0.1459 0.056 0.408 0.184 0.276 0.076
#> GSM152944 3 0.4182 0.6035 0.000 0.000 0.600 0.000 0.400
#> GSM152945 5 0.7122 0.1930 0.000 0.320 0.188 0.032 0.460
#> GSM152946 2 0.4934 0.7175 0.000 0.720 0.192 0.080 0.008
#> GSM152947 4 0.5554 0.4936 0.344 0.000 0.056 0.588 0.012
#> GSM152948 2 0.0609 0.8525 0.000 0.980 0.020 0.000 0.000
#> GSM152949 3 0.3582 0.6727 0.000 0.008 0.768 0.000 0.224
#> GSM152950 3 0.4360 0.6382 0.000 0.024 0.692 0.000 0.284
#> GSM152951 2 0.1750 0.8473 0.000 0.936 0.036 0.028 0.000
#> GSM152952 2 0.0880 0.8485 0.000 0.968 0.032 0.000 0.000
#> GSM152953 2 0.1282 0.8509 0.000 0.952 0.044 0.000 0.004
#> GSM152954 4 0.0566 0.8482 0.000 0.004 0.012 0.984 0.000
#> GSM152955 5 0.4572 0.5937 0.000 0.032 0.128 0.060 0.780
#> GSM152956 2 0.0162 0.8505 0.000 0.996 0.004 0.000 0.000
#> GSM152957 4 0.3995 0.7584 0.180 0.000 0.044 0.776 0.000
#> GSM152958 4 0.1267 0.8473 0.024 0.004 0.012 0.960 0.000
#> GSM152959 4 0.4817 0.3822 0.404 0.000 0.024 0.572 0.000
#> GSM152960 4 0.6807 0.6358 0.136 0.156 0.088 0.616 0.004
#> GSM152961 4 0.1357 0.8449 0.048 0.000 0.004 0.948 0.000
#> GSM152962 3 0.5498 0.4083 0.000 0.076 0.568 0.000 0.356
#> GSM152963 2 0.0290 0.8506 0.000 0.992 0.008 0.000 0.000
#> GSM152964 5 0.2304 0.6635 0.000 0.000 0.100 0.008 0.892
#> GSM152965 2 0.4327 0.7520 0.000 0.780 0.112 0.004 0.104
#> GSM152966 4 0.0671 0.8483 0.000 0.004 0.016 0.980 0.000
#> GSM152967 2 0.4150 0.7325 0.000 0.748 0.216 0.036 0.000
#> GSM152968 3 0.3835 0.6731 0.000 0.008 0.732 0.000 0.260
#> GSM152969 4 0.0451 0.8483 0.000 0.004 0.008 0.988 0.000
#> GSM152970 1 0.4763 0.3757 0.632 0.000 0.032 0.336 0.000
#> GSM152971 4 0.0671 0.8485 0.000 0.004 0.016 0.980 0.000
#> GSM152972 4 0.0566 0.8475 0.000 0.004 0.012 0.984 0.000
#> GSM152973 3 0.5218 0.3827 0.000 0.000 0.632 0.296 0.072
#> GSM152974 2 0.3424 0.7049 0.000 0.760 0.240 0.000 0.000
#> GSM152975 2 0.7891 0.2390 0.000 0.420 0.100 0.288 0.192
#> GSM152976 4 0.3270 0.8226 0.100 0.000 0.044 0.852 0.004
#> GSM152977 4 0.3733 0.7514 0.008 0.000 0.028 0.808 0.156
#> GSM152978 4 0.3633 0.8116 0.060 0.064 0.028 0.848 0.000
#> GSM152979 3 0.4182 0.5997 0.000 0.000 0.600 0.000 0.400
#> GSM152980 2 0.7087 0.4507 0.000 0.540 0.128 0.256 0.076
#> GSM152981 5 0.0451 0.7163 0.000 0.000 0.008 0.004 0.988
#> GSM152982 4 0.1205 0.8466 0.000 0.000 0.040 0.956 0.004
#> GSM152983 4 0.0865 0.8477 0.000 0.000 0.024 0.972 0.004
#> GSM152984 3 0.4583 0.5890 0.000 0.000 0.748 0.112 0.140
#> GSM152985 4 0.5033 0.2536 0.448 0.000 0.024 0.524 0.004
#> GSM152986 4 0.0451 0.8480 0.000 0.004 0.008 0.988 0.000
#> GSM152987 1 0.0912 0.9541 0.972 0.000 0.016 0.012 0.000
#> GSM152988 4 0.3480 0.6970 0.000 0.000 0.248 0.752 0.000
#> GSM152989 1 0.4173 0.4954 0.688 0.000 0.012 0.300 0.000
#> GSM152990 3 0.3913 0.6629 0.000 0.000 0.676 0.000 0.324
#> GSM152991 5 0.2983 0.6786 0.000 0.032 0.096 0.004 0.868
#> GSM187524 1 0.0510 0.9656 0.984 0.000 0.016 0.000 0.000
#> GSM187525 1 0.0404 0.9647 0.988 0.000 0.012 0.000 0.000
#> GSM187526 1 0.0404 0.9647 0.988 0.000 0.012 0.000 0.000
#> GSM187527 1 0.0290 0.9683 0.992 0.000 0.008 0.000 0.000
#> GSM152856 1 0.0404 0.9678 0.988 0.000 0.012 0.000 0.000
#> GSM152857 1 0.0404 0.9678 0.988 0.000 0.012 0.000 0.000
#> GSM152858 1 0.0162 0.9680 0.996 0.000 0.004 0.000 0.000
#> GSM152859 1 0.0162 0.9680 0.996 0.000 0.004 0.000 0.000
#> GSM152860 1 0.0162 0.9680 0.996 0.000 0.004 0.000 0.000
#> GSM152861 1 0.0000 0.9685 1.000 0.000 0.000 0.000 0.000
#> GSM152862 1 0.0162 0.9680 0.996 0.000 0.004 0.000 0.000
#> GSM152863 1 0.0162 0.9685 0.996 0.000 0.004 0.000 0.000
#> GSM152864 1 0.0000 0.9685 1.000 0.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.9685 1.000 0.000 0.000 0.000 0.000
#> GSM152866 1 0.0404 0.9678 0.988 0.000 0.012 0.000 0.000
#> GSM152867 1 0.0162 0.9685 0.996 0.000 0.004 0.000 0.000
#> GSM152868 1 0.0000 0.9685 1.000 0.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.9685 1.000 0.000 0.000 0.000 0.000
#> GSM152870 1 0.0162 0.9680 0.996 0.000 0.004 0.000 0.000
#> GSM152871 1 0.0162 0.9680 0.996 0.000 0.004 0.000 0.000
#> GSM152872 1 0.0162 0.9680 0.996 0.000 0.004 0.000 0.000
#> GSM152873 1 0.0404 0.9678 0.988 0.000 0.012 0.000 0.000
#> GSM152874 1 0.0404 0.9678 0.988 0.000 0.012 0.000 0.000
#> GSM152875 1 0.0404 0.9678 0.988 0.000 0.012 0.000 0.000
#> GSM152876 1 0.0404 0.9678 0.988 0.000 0.012 0.000 0.000
#> GSM152877 1 0.0404 0.9678 0.988 0.000 0.012 0.000 0.000
#> GSM152878 1 0.0404 0.9678 0.988 0.000 0.012 0.000 0.000
#> GSM152879 1 0.0404 0.9678 0.988 0.000 0.012 0.000 0.000
#> GSM152880 1 0.0404 0.9678 0.988 0.000 0.012 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.4381 0.6416 0.000 0.732 0.128 0.004 0.000 0.136
#> GSM152805 5 0.1341 0.6846 0.000 0.000 0.028 0.000 0.948 0.024
#> GSM152806 5 0.0725 0.6873 0.000 0.000 0.012 0.000 0.976 0.012
#> GSM152807 2 0.1462 0.7468 0.000 0.936 0.008 0.000 0.000 0.056
#> GSM152808 5 0.0508 0.6855 0.000 0.000 0.004 0.000 0.984 0.012
#> GSM152809 2 0.1349 0.7483 0.000 0.940 0.004 0.000 0.000 0.056
#> GSM152810 5 0.2182 0.6301 0.020 0.000 0.004 0.000 0.900 0.076
#> GSM152811 5 0.0508 0.6844 0.000 0.000 0.004 0.000 0.984 0.012
#> GSM152812 2 0.0777 0.7467 0.000 0.972 0.004 0.000 0.000 0.024
#> GSM152813 2 0.1838 0.7448 0.000 0.916 0.016 0.000 0.000 0.068
#> GSM152814 2 0.1616 0.7470 0.000 0.932 0.020 0.000 0.000 0.048
#> GSM152815 2 0.0713 0.7469 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM152816 5 0.6531 0.0818 0.000 0.044 0.336 0.000 0.444 0.176
#> GSM152817 5 0.0622 0.6869 0.000 0.000 0.008 0.000 0.980 0.012
#> GSM152818 5 0.0717 0.6871 0.000 0.000 0.008 0.000 0.976 0.016
#> GSM152819 5 0.6507 0.2062 0.000 0.192 0.080 0.000 0.540 0.188
#> GSM152820 5 0.6506 0.2801 0.000 0.084 0.152 0.000 0.536 0.228
#> GSM152821 2 0.2094 0.7453 0.000 0.900 0.020 0.000 0.000 0.080
#> GSM153115 4 0.1644 0.7417 0.000 0.000 0.004 0.920 0.000 0.076
#> GSM153116 5 0.2237 0.6682 0.000 0.000 0.036 0.000 0.896 0.068
#> GSM153117 5 0.7425 -0.0548 0.000 0.240 0.284 0.000 0.348 0.128
#> GSM153118 2 0.3546 0.7086 0.000 0.808 0.056 0.000 0.008 0.128
#> GSM153119 5 0.2542 0.6471 0.000 0.000 0.044 0.000 0.876 0.080
#> GSM153120 4 0.6649 0.2034 0.276 0.044 0.000 0.448 0.000 0.232
#> GSM153121 3 0.3196 0.7218 0.000 0.000 0.828 0.000 0.108 0.064
#> GSM153122 5 0.3787 0.5756 0.000 0.000 0.120 0.000 0.780 0.100
#> GSM153123 3 0.5822 0.2437 0.000 0.276 0.516 0.000 0.004 0.204
#> GSM153124 4 0.5266 0.5506 0.000 0.060 0.076 0.676 0.000 0.188
#> GSM153125 4 0.1701 0.7460 0.000 0.008 0.000 0.920 0.000 0.072
#> GSM153126 3 0.3066 0.7193 0.000 0.000 0.832 0.000 0.124 0.044
#> GSM153127 2 0.1297 0.7474 0.000 0.948 0.012 0.000 0.000 0.040
#> GSM153128 5 0.5372 0.4090 0.000 0.012 0.176 0.000 0.628 0.184
#> GSM153129 3 0.3988 0.7003 0.000 0.040 0.804 0.004 0.060 0.092
#> GSM153130 3 0.3592 0.6702 0.000 0.000 0.740 0.000 0.240 0.020
#> GSM153131 3 0.6009 0.4760 0.000 0.024 0.544 0.000 0.252 0.180
#> GSM153132 3 0.5811 0.2805 0.000 0.008 0.492 0.000 0.348 0.152
#> GSM153133 3 0.5890 0.1609 0.000 0.300 0.508 0.000 0.008 0.184
#> GSM153134 3 0.4335 0.6501 0.000 0.080 0.764 0.000 0.032 0.124
#> GSM153135 2 0.1327 0.7409 0.000 0.936 0.000 0.000 0.000 0.064
#> GSM153136 4 0.1267 0.7475 0.000 0.000 0.000 0.940 0.000 0.060
#> GSM153137 2 0.2357 0.7171 0.000 0.872 0.000 0.012 0.000 0.116
#> GSM153138 2 0.4260 0.5897 0.000 0.692 0.016 0.004 0.016 0.272
#> GSM153139 3 0.3572 0.6960 0.000 0.000 0.764 0.000 0.204 0.032
#> GSM153140 2 0.5591 0.5456 0.000 0.628 0.116 0.040 0.000 0.216
#> GSM153141 2 0.1010 0.7475 0.000 0.960 0.004 0.000 0.000 0.036
#> GSM153142 5 0.2060 0.6636 0.000 0.000 0.084 0.000 0.900 0.016
#> GSM153143 2 0.5079 0.5091 0.000 0.672 0.028 0.088 0.000 0.212
#> GSM153144 3 0.5119 0.3181 0.000 0.308 0.584 0.000 0.000 0.108
#> GSM153145 5 0.0622 0.6869 0.000 0.000 0.008 0.000 0.980 0.012
#> GSM153146 2 0.3010 0.7252 0.000 0.836 0.028 0.000 0.004 0.132
#> GSM153147 3 0.2739 0.6979 0.000 0.012 0.872 0.000 0.032 0.084
#> GSM153148 2 0.1141 0.7442 0.000 0.948 0.000 0.000 0.000 0.052
#> GSM153149 2 0.6354 0.2685 0.000 0.500 0.268 0.000 0.036 0.196
#> GSM153150 4 0.4530 0.5962 0.136 0.000 0.000 0.704 0.000 0.160
#> GSM153151 3 0.7232 0.0117 0.000 0.116 0.412 0.004 0.164 0.304
#> GSM153152 3 0.5289 0.5539 0.000 0.140 0.684 0.000 0.052 0.124
#> GSM153153 2 0.3997 0.6761 0.000 0.764 0.080 0.000 0.004 0.152
#> GSM153154 3 0.4599 0.6286 0.000 0.000 0.684 0.000 0.212 0.104
#> GSM153155 2 0.4201 0.6720 0.000 0.740 0.080 0.000 0.004 0.176
#> GSM153156 3 0.4085 0.6968 0.000 0.000 0.736 0.000 0.192 0.072
#> GSM153157 5 0.1549 0.6829 0.000 0.000 0.044 0.000 0.936 0.020
#> GSM153158 5 0.5562 0.3096 0.000 0.024 0.320 0.000 0.564 0.092
#> GSM153159 5 0.4139 0.3351 0.000 0.000 0.336 0.000 0.640 0.024
#> GSM153160 3 0.2872 0.7223 0.000 0.000 0.836 0.000 0.140 0.024
#> GSM153161 2 0.1556 0.7359 0.000 0.920 0.000 0.000 0.000 0.080
#> GSM153162 3 0.2444 0.6986 0.000 0.012 0.892 0.000 0.028 0.068
#> GSM153163 3 0.3834 0.6423 0.000 0.000 0.708 0.000 0.268 0.024
#> GSM153164 5 0.7586 -0.1112 0.000 0.256 0.164 0.000 0.324 0.256
#> GSM153165 3 0.3014 0.7233 0.000 0.000 0.832 0.000 0.132 0.036
#> GSM153166 3 0.6262 0.0374 0.000 0.356 0.436 0.000 0.020 0.188
#> GSM153167 3 0.4902 0.5709 0.000 0.092 0.708 0.004 0.024 0.172
#> GSM153168 5 0.0146 0.6847 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM153169 3 0.4437 0.4447 0.000 0.000 0.576 0.000 0.392 0.032
#> GSM153170 3 0.2706 0.7273 0.000 0.000 0.860 0.000 0.104 0.036
#> GSM153171 4 0.3090 0.7331 0.028 0.000 0.004 0.828 0.000 0.140
#> GSM153172 2 0.2937 0.7331 0.000 0.848 0.056 0.000 0.000 0.096
#> GSM153173 3 0.3017 0.7175 0.000 0.000 0.816 0.000 0.164 0.020
#> GSM153174 3 0.2586 0.6704 0.000 0.032 0.868 0.000 0.000 0.100
#> GSM153175 4 0.2309 0.7306 0.000 0.000 0.028 0.888 0.000 0.084
#> GSM153176 4 0.7591 0.1822 0.044 0.000 0.208 0.472 0.112 0.164
#> GSM153177 2 0.6782 0.2045 0.000 0.456 0.284 0.000 0.068 0.192
#> GSM152931 4 0.1333 0.7447 0.000 0.000 0.008 0.944 0.000 0.048
#> GSM152932 2 0.6512 0.0872 0.000 0.404 0.348 0.000 0.028 0.220
#> GSM152933 2 0.5053 0.6163 0.000 0.700 0.096 0.000 0.044 0.160
#> GSM152934 6 0.8123 0.3762 0.052 0.032 0.088 0.248 0.136 0.444
#> GSM152935 6 0.7663 0.2509 0.000 0.208 0.212 0.000 0.280 0.300
#> GSM152936 4 0.3348 0.6993 0.020 0.016 0.000 0.812 0.000 0.152
#> GSM152937 5 0.6230 -0.0275 0.000 0.004 0.324 0.000 0.372 0.300
#> GSM152938 3 0.4658 0.6441 0.000 0.004 0.700 0.000 0.128 0.168
#> GSM152939 4 0.4283 0.5674 0.000 0.000 0.180 0.724 0.000 0.096
#> GSM152940 4 0.5150 0.4938 0.220 0.000 0.000 0.620 0.000 0.160
#> GSM152941 1 0.2956 0.8372 0.848 0.000 0.000 0.064 0.000 0.088
#> GSM152942 3 0.3271 0.7106 0.000 0.000 0.844 0.020 0.076 0.060
#> GSM152943 6 0.7158 0.4526 0.008 0.260 0.020 0.172 0.056 0.484
#> GSM152944 3 0.3483 0.6966 0.000 0.000 0.764 0.000 0.212 0.024
#> GSM152945 6 0.6944 0.4561 0.000 0.168 0.024 0.044 0.300 0.464
#> GSM152946 2 0.6635 0.1489 0.000 0.488 0.124 0.092 0.000 0.296
#> GSM152947 4 0.5560 0.3902 0.320 0.000 0.004 0.536 0.000 0.140
#> GSM152948 2 0.1411 0.7468 0.000 0.936 0.004 0.000 0.000 0.060
#> GSM152949 3 0.2451 0.7100 0.000 0.000 0.884 0.000 0.060 0.056
#> GSM152950 3 0.5238 0.5937 0.000 0.024 0.664 0.000 0.176 0.136
#> GSM152951 2 0.2500 0.7334 0.000 0.868 0.012 0.004 0.000 0.116
#> GSM152952 2 0.1863 0.7273 0.000 0.896 0.000 0.000 0.000 0.104
#> GSM152953 2 0.2165 0.7397 0.000 0.884 0.008 0.000 0.000 0.108
#> GSM152954 4 0.2101 0.7389 0.004 0.000 0.004 0.892 0.000 0.100
#> GSM152955 5 0.5453 0.2814 0.000 0.004 0.036 0.072 0.624 0.264
#> GSM152956 2 0.0790 0.7430 0.000 0.968 0.000 0.000 0.000 0.032
#> GSM152957 4 0.5065 0.5852 0.196 0.000 0.012 0.664 0.000 0.128
#> GSM152958 4 0.1461 0.7445 0.016 0.000 0.000 0.940 0.000 0.044
#> GSM152959 4 0.5248 0.3172 0.404 0.000 0.004 0.508 0.000 0.084
#> GSM152960 4 0.6789 0.2376 0.116 0.136 0.000 0.496 0.000 0.252
#> GSM152961 4 0.2197 0.7384 0.056 0.000 0.000 0.900 0.000 0.044
#> GSM152962 3 0.6758 0.1485 0.000 0.048 0.428 0.000 0.264 0.260
#> GSM152963 2 0.1387 0.7403 0.000 0.932 0.000 0.000 0.000 0.068
#> GSM152964 5 0.3159 0.5636 0.000 0.004 0.012 0.004 0.812 0.168
#> GSM152965 2 0.6036 0.2975 0.000 0.556 0.076 0.004 0.064 0.300
#> GSM152966 4 0.1010 0.7456 0.000 0.000 0.004 0.960 0.000 0.036
#> GSM152967 2 0.6169 0.4187 0.000 0.580 0.200 0.048 0.004 0.168
#> GSM152968 3 0.2457 0.7225 0.000 0.000 0.880 0.000 0.084 0.036
#> GSM152969 4 0.1219 0.7456 0.000 0.000 0.004 0.948 0.000 0.048
#> GSM152970 1 0.4915 0.4410 0.632 0.000 0.000 0.260 0.000 0.108
#> GSM152971 4 0.0547 0.7448 0.000 0.000 0.000 0.980 0.000 0.020
#> GSM152972 4 0.0547 0.7448 0.000 0.000 0.000 0.980 0.000 0.020
#> GSM152973 3 0.4420 0.5228 0.000 0.000 0.728 0.172 0.008 0.092
#> GSM152974 2 0.4974 0.5211 0.000 0.644 0.212 0.000 0.000 0.144
#> GSM152975 2 0.8138 -0.1829 0.000 0.400 0.060 0.168 0.208 0.164
#> GSM152976 4 0.3864 0.7117 0.076 0.000 0.016 0.812 0.012 0.084
#> GSM152977 4 0.4624 0.5849 0.004 0.000 0.004 0.716 0.152 0.124
#> GSM152978 4 0.4584 0.6466 0.040 0.044 0.008 0.744 0.000 0.164
#> GSM152979 3 0.3377 0.7044 0.000 0.000 0.784 0.000 0.188 0.028
#> GSM152980 2 0.7964 -0.1091 0.000 0.344 0.072 0.204 0.068 0.312
#> GSM152981 5 0.0717 0.6806 0.000 0.000 0.008 0.000 0.976 0.016
#> GSM152982 4 0.2215 0.7386 0.000 0.000 0.012 0.900 0.012 0.076
#> GSM152983 4 0.0937 0.7462 0.000 0.000 0.000 0.960 0.000 0.040
#> GSM152984 3 0.4288 0.6151 0.000 0.004 0.768 0.080 0.020 0.128
#> GSM152985 4 0.5198 0.3470 0.380 0.000 0.000 0.524 0.000 0.096
#> GSM152986 4 0.0777 0.7459 0.004 0.000 0.000 0.972 0.000 0.024
#> GSM152987 1 0.2191 0.8816 0.876 0.000 0.000 0.004 0.000 0.120
#> GSM152988 4 0.4769 0.4335 0.000 0.000 0.264 0.644 0.000 0.092
#> GSM152989 1 0.4844 0.3444 0.608 0.000 0.000 0.312 0.000 0.080
#> GSM152990 3 0.2664 0.7265 0.000 0.000 0.848 0.000 0.136 0.016
#> GSM152991 5 0.3760 0.6043 0.000 0.020 0.052 0.000 0.800 0.128
#> GSM187524 1 0.1204 0.9322 0.944 0.000 0.000 0.000 0.000 0.056
#> GSM187525 1 0.1204 0.9265 0.944 0.000 0.000 0.000 0.000 0.056
#> GSM187526 1 0.0713 0.9355 0.972 0.000 0.000 0.000 0.000 0.028
#> GSM187527 1 0.0935 0.9377 0.964 0.000 0.004 0.000 0.000 0.032
#> GSM152856 1 0.1152 0.9354 0.952 0.000 0.004 0.000 0.000 0.044
#> GSM152857 1 0.1226 0.9343 0.952 0.000 0.004 0.000 0.004 0.040
#> GSM152858 1 0.0790 0.9344 0.968 0.000 0.000 0.000 0.000 0.032
#> GSM152859 1 0.1075 0.9290 0.952 0.000 0.000 0.000 0.000 0.048
#> GSM152860 1 0.0865 0.9332 0.964 0.000 0.000 0.000 0.000 0.036
#> GSM152861 1 0.0000 0.9395 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152862 1 0.0865 0.9332 0.964 0.000 0.000 0.000 0.000 0.036
#> GSM152863 1 0.0260 0.9395 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM152864 1 0.0000 0.9395 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.9395 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152866 1 0.1219 0.9371 0.948 0.000 0.004 0.000 0.000 0.048
#> GSM152867 1 0.0146 0.9396 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM152868 1 0.0000 0.9395 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.9395 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152870 1 0.0865 0.9332 0.964 0.000 0.000 0.000 0.000 0.036
#> GSM152871 1 0.0790 0.9344 0.968 0.000 0.000 0.000 0.000 0.032
#> GSM152872 1 0.0865 0.9332 0.964 0.000 0.000 0.000 0.000 0.036
#> GSM152873 1 0.1152 0.9354 0.952 0.000 0.004 0.000 0.000 0.044
#> GSM152874 1 0.1152 0.9354 0.952 0.000 0.004 0.000 0.000 0.044
#> GSM152875 1 0.1152 0.9354 0.952 0.000 0.004 0.000 0.000 0.044
#> GSM152876 1 0.1152 0.9354 0.952 0.000 0.004 0.000 0.000 0.044
#> GSM152877 1 0.1152 0.9354 0.952 0.000 0.004 0.000 0.000 0.044
#> GSM152878 1 0.1152 0.9354 0.952 0.000 0.004 0.000 0.000 0.044
#> GSM152879 1 0.1152 0.9354 0.952 0.000 0.004 0.000 0.000 0.044
#> GSM152880 1 0.1152 0.9354 0.952 0.000 0.004 0.000 0.000 0.044
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> MAD:skmeans 169 2.27e-14 2
#> MAD:skmeans 158 1.81e-13 3
#> MAD:skmeans 157 1.17e-26 4
#> MAD:skmeans 137 4.85e-25 5
#> MAD:skmeans 130 4.10e-24 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "pam"]
# you can also extract it by
# res = res_list["MAD:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.969 0.987 0.3195 0.694 0.694
#> 3 3 0.509 0.665 0.820 0.9008 0.699 0.570
#> 4 4 0.469 0.581 0.713 0.1113 0.957 0.898
#> 5 5 0.520 0.609 0.743 0.0832 0.809 0.531
#> 6 6 0.548 0.609 0.744 0.0387 0.900 0.653
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.9852 0.000 1.000
#> GSM152805 2 0.0000 0.9852 0.000 1.000
#> GSM152806 2 0.0000 0.9852 0.000 1.000
#> GSM152807 2 0.0000 0.9852 0.000 1.000
#> GSM152808 2 0.0000 0.9852 0.000 1.000
#> GSM152809 2 0.0000 0.9852 0.000 1.000
#> GSM152810 2 0.0000 0.9852 0.000 1.000
#> GSM152811 2 0.0000 0.9852 0.000 1.000
#> GSM152812 2 0.0000 0.9852 0.000 1.000
#> GSM152813 2 0.0000 0.9852 0.000 1.000
#> GSM152814 2 0.0000 0.9852 0.000 1.000
#> GSM152815 2 0.0000 0.9852 0.000 1.000
#> GSM152816 2 0.0000 0.9852 0.000 1.000
#> GSM152817 2 0.0000 0.9852 0.000 1.000
#> GSM152818 2 0.0000 0.9852 0.000 1.000
#> GSM152819 2 0.0000 0.9852 0.000 1.000
#> GSM152820 2 0.0000 0.9852 0.000 1.000
#> GSM152821 2 0.0000 0.9852 0.000 1.000
#> GSM153115 2 0.0000 0.9852 0.000 1.000
#> GSM153116 2 0.0000 0.9852 0.000 1.000
#> GSM153117 2 0.0000 0.9852 0.000 1.000
#> GSM153118 2 0.0000 0.9852 0.000 1.000
#> GSM153119 2 0.0000 0.9852 0.000 1.000
#> GSM153120 2 0.5178 0.8684 0.116 0.884
#> GSM153121 2 0.0000 0.9852 0.000 1.000
#> GSM153122 2 0.0000 0.9852 0.000 1.000
#> GSM153123 2 0.0000 0.9852 0.000 1.000
#> GSM153124 2 0.0000 0.9852 0.000 1.000
#> GSM153125 2 0.0000 0.9852 0.000 1.000
#> GSM153126 2 0.0000 0.9852 0.000 1.000
#> GSM153127 2 0.0000 0.9852 0.000 1.000
#> GSM153128 2 0.0000 0.9852 0.000 1.000
#> GSM153129 2 0.0000 0.9852 0.000 1.000
#> GSM153130 2 0.0000 0.9852 0.000 1.000
#> GSM153131 2 0.0000 0.9852 0.000 1.000
#> GSM153132 2 0.0000 0.9852 0.000 1.000
#> GSM153133 2 0.0000 0.9852 0.000 1.000
#> GSM153134 2 0.0000 0.9852 0.000 1.000
#> GSM153135 2 0.0000 0.9852 0.000 1.000
#> GSM153136 2 0.0000 0.9852 0.000 1.000
#> GSM153137 2 0.0000 0.9852 0.000 1.000
#> GSM153138 2 0.0000 0.9852 0.000 1.000
#> GSM153139 2 0.0000 0.9852 0.000 1.000
#> GSM153140 2 0.0000 0.9852 0.000 1.000
#> GSM153141 2 0.0000 0.9852 0.000 1.000
#> GSM153142 2 0.0000 0.9852 0.000 1.000
#> GSM153143 2 0.0000 0.9852 0.000 1.000
#> GSM153144 2 0.0000 0.9852 0.000 1.000
#> GSM153145 2 0.0000 0.9852 0.000 1.000
#> GSM153146 2 0.0000 0.9852 0.000 1.000
#> GSM153147 2 0.0000 0.9852 0.000 1.000
#> GSM153148 2 0.0000 0.9852 0.000 1.000
#> GSM153149 2 0.0000 0.9852 0.000 1.000
#> GSM153150 2 0.4161 0.9049 0.084 0.916
#> GSM153151 2 0.0000 0.9852 0.000 1.000
#> GSM153152 2 0.0000 0.9852 0.000 1.000
#> GSM153153 2 0.0000 0.9852 0.000 1.000
#> GSM153154 2 0.0000 0.9852 0.000 1.000
#> GSM153155 2 0.0000 0.9852 0.000 1.000
#> GSM153156 2 0.0000 0.9852 0.000 1.000
#> GSM153157 2 0.0000 0.9852 0.000 1.000
#> GSM153158 2 0.0000 0.9852 0.000 1.000
#> GSM153159 2 0.0000 0.9852 0.000 1.000
#> GSM153160 2 0.0000 0.9852 0.000 1.000
#> GSM153161 2 0.0000 0.9852 0.000 1.000
#> GSM153162 2 0.0000 0.9852 0.000 1.000
#> GSM153163 2 0.0000 0.9852 0.000 1.000
#> GSM153164 2 0.0000 0.9852 0.000 1.000
#> GSM153165 2 0.0000 0.9852 0.000 1.000
#> GSM153166 2 0.0000 0.9852 0.000 1.000
#> GSM153167 2 0.0000 0.9852 0.000 1.000
#> GSM153168 2 0.0000 0.9852 0.000 1.000
#> GSM153169 2 0.0000 0.9852 0.000 1.000
#> GSM153170 2 0.0000 0.9852 0.000 1.000
#> GSM153171 2 0.0938 0.9753 0.012 0.988
#> GSM153172 2 0.0000 0.9852 0.000 1.000
#> GSM153173 2 0.0000 0.9852 0.000 1.000
#> GSM153174 2 0.0000 0.9852 0.000 1.000
#> GSM153175 2 0.0000 0.9852 0.000 1.000
#> GSM153176 2 0.0000 0.9852 0.000 1.000
#> GSM153177 2 0.0000 0.9852 0.000 1.000
#> GSM152931 2 0.0000 0.9852 0.000 1.000
#> GSM152932 2 0.0000 0.9852 0.000 1.000
#> GSM152933 2 0.0000 0.9852 0.000 1.000
#> GSM152934 2 0.0000 0.9852 0.000 1.000
#> GSM152935 2 0.0000 0.9852 0.000 1.000
#> GSM152936 2 0.0000 0.9852 0.000 1.000
#> GSM152937 2 0.0000 0.9852 0.000 1.000
#> GSM152938 2 0.0000 0.9852 0.000 1.000
#> GSM152939 2 0.1843 0.9612 0.028 0.972
#> GSM152940 2 0.7219 0.7558 0.200 0.800
#> GSM152941 1 0.0672 0.9868 0.992 0.008
#> GSM152942 2 0.0000 0.9852 0.000 1.000
#> GSM152943 2 0.0000 0.9852 0.000 1.000
#> GSM152944 2 0.0000 0.9852 0.000 1.000
#> GSM152945 2 0.0000 0.9852 0.000 1.000
#> GSM152946 2 0.0000 0.9852 0.000 1.000
#> GSM152947 2 0.3274 0.9303 0.060 0.940
#> GSM152948 2 0.0000 0.9852 0.000 1.000
#> GSM152949 2 0.0000 0.9852 0.000 1.000
#> GSM152950 2 0.0000 0.9852 0.000 1.000
#> GSM152951 2 0.0000 0.9852 0.000 1.000
#> GSM152952 2 0.0000 0.9852 0.000 1.000
#> GSM152953 2 0.0000 0.9852 0.000 1.000
#> GSM152954 2 0.0000 0.9852 0.000 1.000
#> GSM152955 2 0.0000 0.9852 0.000 1.000
#> GSM152956 2 0.0000 0.9852 0.000 1.000
#> GSM152957 2 0.1414 0.9682 0.020 0.980
#> GSM152958 2 0.9996 0.0679 0.488 0.512
#> GSM152959 2 0.3114 0.9343 0.056 0.944
#> GSM152960 2 0.0000 0.9852 0.000 1.000
#> GSM152961 2 0.9460 0.4436 0.364 0.636
#> GSM152962 2 0.0000 0.9852 0.000 1.000
#> GSM152963 2 0.0000 0.9852 0.000 1.000
#> GSM152964 2 0.0000 0.9852 0.000 1.000
#> GSM152965 2 0.0000 0.9852 0.000 1.000
#> GSM152966 2 0.3431 0.9260 0.064 0.936
#> GSM152967 2 0.0000 0.9852 0.000 1.000
#> GSM152968 2 0.0000 0.9852 0.000 1.000
#> GSM152969 2 0.0000 0.9852 0.000 1.000
#> GSM152970 2 0.6343 0.8124 0.160 0.840
#> GSM152971 2 0.0000 0.9852 0.000 1.000
#> GSM152972 2 0.0000 0.9852 0.000 1.000
#> GSM152973 2 0.0000 0.9852 0.000 1.000
#> GSM152974 2 0.0000 0.9852 0.000 1.000
#> GSM152975 2 0.0000 0.9852 0.000 1.000
#> GSM152976 2 0.0000 0.9852 0.000 1.000
#> GSM152977 2 0.0000 0.9852 0.000 1.000
#> GSM152978 2 0.0672 0.9786 0.008 0.992
#> GSM152979 2 0.0000 0.9852 0.000 1.000
#> GSM152980 2 0.0000 0.9852 0.000 1.000
#> GSM152981 2 0.0000 0.9852 0.000 1.000
#> GSM152982 2 0.0000 0.9852 0.000 1.000
#> GSM152983 2 0.0000 0.9852 0.000 1.000
#> GSM152984 2 0.0000 0.9852 0.000 1.000
#> GSM152985 1 0.0000 0.9933 1.000 0.000
#> GSM152986 2 0.0938 0.9752 0.012 0.988
#> GSM152987 1 0.2043 0.9645 0.968 0.032
#> GSM152988 2 0.0000 0.9852 0.000 1.000
#> GSM152989 1 0.5737 0.8396 0.864 0.136
#> GSM152990 2 0.0000 0.9852 0.000 1.000
#> GSM152991 2 0.0000 0.9852 0.000 1.000
#> GSM187524 1 0.0000 0.9933 1.000 0.000
#> GSM187525 1 0.0000 0.9933 1.000 0.000
#> GSM187526 1 0.0000 0.9933 1.000 0.000
#> GSM187527 1 0.1633 0.9722 0.976 0.024
#> GSM152856 1 0.0000 0.9933 1.000 0.000
#> GSM152857 2 0.9427 0.4544 0.360 0.640
#> GSM152858 1 0.0000 0.9933 1.000 0.000
#> GSM152859 1 0.0000 0.9933 1.000 0.000
#> GSM152860 1 0.0000 0.9933 1.000 0.000
#> GSM152861 1 0.0000 0.9933 1.000 0.000
#> GSM152862 1 0.0000 0.9933 1.000 0.000
#> GSM152863 1 0.0000 0.9933 1.000 0.000
#> GSM152864 1 0.0000 0.9933 1.000 0.000
#> GSM152865 1 0.0000 0.9933 1.000 0.000
#> GSM152866 1 0.0000 0.9933 1.000 0.000
#> GSM152867 1 0.0000 0.9933 1.000 0.000
#> GSM152868 1 0.0000 0.9933 1.000 0.000
#> GSM152869 1 0.0000 0.9933 1.000 0.000
#> GSM152870 1 0.0000 0.9933 1.000 0.000
#> GSM152871 1 0.0000 0.9933 1.000 0.000
#> GSM152872 1 0.0000 0.9933 1.000 0.000
#> GSM152873 1 0.0000 0.9933 1.000 0.000
#> GSM152874 1 0.0000 0.9933 1.000 0.000
#> GSM152875 1 0.0000 0.9933 1.000 0.000
#> GSM152876 1 0.0000 0.9933 1.000 0.000
#> GSM152877 1 0.0000 0.9933 1.000 0.000
#> GSM152878 1 0.0000 0.9933 1.000 0.000
#> GSM152879 1 0.0000 0.9933 1.000 0.000
#> GSM152880 1 0.0000 0.9933 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 3 0.6008 0.631619 0.000 0.372 0.628
#> GSM152805 3 0.1163 0.678853 0.000 0.028 0.972
#> GSM152806 3 0.0747 0.676037 0.000 0.016 0.984
#> GSM152807 3 0.6244 0.595387 0.000 0.440 0.560
#> GSM152808 3 0.0237 0.670225 0.000 0.004 0.996
#> GSM152809 2 0.5760 0.073111 0.000 0.672 0.328
#> GSM152810 3 0.6274 0.029953 0.000 0.456 0.544
#> GSM152811 3 0.2796 0.634586 0.000 0.092 0.908
#> GSM152812 3 0.6140 0.619320 0.000 0.404 0.596
#> GSM152813 3 0.6008 0.633948 0.000 0.372 0.628
#> GSM152814 3 0.6140 0.619320 0.000 0.404 0.596
#> GSM152815 3 0.6244 0.595387 0.000 0.440 0.560
#> GSM152816 3 0.1860 0.681807 0.000 0.052 0.948
#> GSM152817 3 0.2261 0.674698 0.000 0.068 0.932
#> GSM152818 3 0.0237 0.672657 0.000 0.004 0.996
#> GSM152819 3 0.4974 0.684818 0.000 0.236 0.764
#> GSM152820 3 0.1031 0.682213 0.000 0.024 0.976
#> GSM152821 3 0.6204 0.608422 0.000 0.424 0.576
#> GSM153115 2 0.2165 0.756301 0.000 0.936 0.064
#> GSM153116 3 0.3551 0.685973 0.000 0.132 0.868
#> GSM153117 3 0.5948 0.643720 0.000 0.360 0.640
#> GSM153118 3 0.6079 0.628038 0.000 0.388 0.612
#> GSM153119 3 0.2625 0.671469 0.000 0.084 0.916
#> GSM153120 2 0.1525 0.779663 0.004 0.964 0.032
#> GSM153121 3 0.3340 0.643365 0.000 0.120 0.880
#> GSM153122 3 0.2165 0.652075 0.000 0.064 0.936
#> GSM153123 3 0.5905 0.643988 0.000 0.352 0.648
#> GSM153124 3 0.6295 0.536707 0.000 0.472 0.528
#> GSM153125 2 0.1529 0.766771 0.000 0.960 0.040
#> GSM153126 2 0.6267 0.359221 0.000 0.548 0.452
#> GSM153127 3 0.6111 0.614868 0.000 0.396 0.604
#> GSM153128 3 0.4178 0.688427 0.000 0.172 0.828
#> GSM153129 3 0.1289 0.678552 0.000 0.032 0.968
#> GSM153130 3 0.0237 0.669706 0.000 0.004 0.996
#> GSM153131 3 0.2796 0.662694 0.000 0.092 0.908
#> GSM153132 3 0.1411 0.680163 0.000 0.036 0.964
#> GSM153133 3 0.6180 0.607351 0.000 0.416 0.584
#> GSM153134 3 0.4654 0.688522 0.000 0.208 0.792
#> GSM153135 3 0.6252 0.593518 0.000 0.444 0.556
#> GSM153136 2 0.0000 0.780757 0.000 1.000 0.000
#> GSM153137 3 0.6180 0.613749 0.000 0.416 0.584
#> GSM153138 3 0.6126 0.621604 0.000 0.400 0.600
#> GSM153139 3 0.1964 0.682276 0.000 0.056 0.944
#> GSM153140 3 0.5968 0.635734 0.000 0.364 0.636
#> GSM153141 3 0.6168 0.616109 0.000 0.412 0.588
#> GSM153142 3 0.1411 0.669933 0.000 0.036 0.964
#> GSM153143 3 0.6280 0.558309 0.000 0.460 0.540
#> GSM153144 2 0.5591 0.259200 0.000 0.696 0.304
#> GSM153145 3 0.0237 0.669706 0.000 0.004 0.996
#> GSM153146 3 0.6126 0.622099 0.000 0.400 0.600
#> GSM153147 2 0.6008 0.226909 0.000 0.628 0.372
#> GSM153148 3 0.6204 0.608814 0.000 0.424 0.576
#> GSM153149 3 0.6062 0.631760 0.000 0.384 0.616
#> GSM153150 2 0.0237 0.779875 0.000 0.996 0.004
#> GSM153151 3 0.5678 0.660664 0.000 0.316 0.684
#> GSM153152 3 0.6045 0.598896 0.000 0.380 0.620
#> GSM153153 3 0.6192 0.611491 0.000 0.420 0.580
#> GSM153154 3 0.3941 0.599271 0.000 0.156 0.844
#> GSM153155 3 0.6225 0.600724 0.000 0.432 0.568
#> GSM153156 3 0.0424 0.672428 0.000 0.008 0.992
#> GSM153157 3 0.0424 0.669401 0.000 0.008 0.992
#> GSM153158 3 0.5058 0.685935 0.000 0.244 0.756
#> GSM153159 3 0.1860 0.675882 0.000 0.052 0.948
#> GSM153160 3 0.5497 0.261675 0.000 0.292 0.708
#> GSM153161 3 0.6267 0.584029 0.000 0.452 0.548
#> GSM153162 2 0.3482 0.727746 0.000 0.872 0.128
#> GSM153163 3 0.1860 0.681223 0.000 0.052 0.948
#> GSM153164 3 0.5760 0.660733 0.000 0.328 0.672
#> GSM153165 3 0.1643 0.680161 0.000 0.044 0.956
#> GSM153166 3 0.3686 0.692494 0.000 0.140 0.860
#> GSM153167 3 0.3267 0.693388 0.000 0.116 0.884
#> GSM153168 3 0.0237 0.670506 0.000 0.004 0.996
#> GSM153169 3 0.0000 0.670651 0.000 0.000 1.000
#> GSM153170 3 0.0237 0.672706 0.000 0.004 0.996
#> GSM153171 2 0.0237 0.780115 0.000 0.996 0.004
#> GSM153172 3 0.6111 0.624134 0.000 0.396 0.604
#> GSM153173 3 0.4121 0.517193 0.000 0.168 0.832
#> GSM153174 2 0.2448 0.766194 0.000 0.924 0.076
#> GSM153175 2 0.1529 0.780312 0.000 0.960 0.040
#> GSM153176 2 0.6079 0.414256 0.000 0.612 0.388
#> GSM153177 3 0.5560 0.670955 0.000 0.300 0.700
#> GSM152931 2 0.0892 0.783010 0.000 0.980 0.020
#> GSM152932 3 0.4974 0.683994 0.000 0.236 0.764
#> GSM152933 3 0.5254 0.677947 0.000 0.264 0.736
#> GSM152934 2 0.2165 0.767559 0.000 0.936 0.064
#> GSM152935 3 0.6126 0.626747 0.000 0.400 0.600
#> GSM152936 2 0.0424 0.779636 0.000 0.992 0.008
#> GSM152937 3 0.3340 0.663879 0.000 0.120 0.880
#> GSM152938 3 0.4121 0.600675 0.000 0.168 0.832
#> GSM152939 2 0.0424 0.782920 0.000 0.992 0.008
#> GSM152940 2 0.1620 0.780174 0.012 0.964 0.024
#> GSM152941 1 0.1525 0.942665 0.964 0.032 0.004
#> GSM152942 2 0.6062 0.419148 0.000 0.616 0.384
#> GSM152943 3 0.6299 0.536923 0.000 0.476 0.524
#> GSM152944 3 0.0892 0.674772 0.000 0.020 0.980
#> GSM152945 3 0.6126 0.611134 0.000 0.400 0.600
#> GSM152946 3 0.6244 0.581975 0.000 0.440 0.560
#> GSM152947 2 0.1636 0.781923 0.020 0.964 0.016
#> GSM152948 3 0.6140 0.619320 0.000 0.404 0.596
#> GSM152949 3 0.6280 -0.198227 0.000 0.460 0.540
#> GSM152950 2 0.6299 0.276974 0.000 0.524 0.476
#> GSM152951 2 0.6308 -0.498432 0.000 0.508 0.492
#> GSM152952 3 0.6267 0.584056 0.000 0.452 0.548
#> GSM152953 3 0.6026 0.633104 0.000 0.376 0.624
#> GSM152954 2 0.4654 0.556270 0.000 0.792 0.208
#> GSM152955 3 0.2796 0.690363 0.000 0.092 0.908
#> GSM152956 3 0.6140 0.619320 0.000 0.404 0.596
#> GSM152957 2 0.0237 0.780115 0.000 0.996 0.004
#> GSM152958 2 0.1163 0.779289 0.028 0.972 0.000
#> GSM152959 2 0.0424 0.782269 0.008 0.992 0.000
#> GSM152960 2 0.5058 0.385770 0.000 0.756 0.244
#> GSM152961 2 0.2590 0.753976 0.072 0.924 0.004
#> GSM152962 3 0.6095 0.622280 0.000 0.392 0.608
#> GSM152963 3 0.6204 0.608795 0.000 0.424 0.576
#> GSM152964 3 0.4887 0.554639 0.000 0.228 0.772
#> GSM152965 3 0.6111 0.614868 0.000 0.396 0.604
#> GSM152966 2 0.0237 0.782447 0.000 0.996 0.004
#> GSM152967 2 0.1289 0.780348 0.000 0.968 0.032
#> GSM152968 3 0.0237 0.672657 0.000 0.004 0.996
#> GSM152969 2 0.5291 0.390672 0.000 0.732 0.268
#> GSM152970 2 0.4642 0.733903 0.084 0.856 0.060
#> GSM152971 2 0.0237 0.782447 0.000 0.996 0.004
#> GSM152972 2 0.0424 0.782792 0.000 0.992 0.008
#> GSM152973 2 0.5968 0.433523 0.000 0.636 0.364
#> GSM152974 3 0.6204 0.610275 0.000 0.424 0.576
#> GSM152975 2 0.3412 0.665355 0.000 0.876 0.124
#> GSM152976 2 0.1753 0.768881 0.000 0.952 0.048
#> GSM152977 3 0.6280 -0.218478 0.000 0.460 0.540
#> GSM152978 2 0.4629 0.559884 0.004 0.808 0.188
#> GSM152979 3 0.0892 0.674798 0.000 0.020 0.980
#> GSM152980 3 0.5760 0.656521 0.000 0.328 0.672
#> GSM152981 3 0.2448 0.674582 0.000 0.076 0.924
#> GSM152982 2 0.2448 0.759678 0.000 0.924 0.076
#> GSM152983 2 0.0747 0.782996 0.000 0.984 0.016
#> GSM152984 2 0.2959 0.736458 0.000 0.900 0.100
#> GSM152985 2 0.6476 -0.000692 0.448 0.548 0.004
#> GSM152986 2 0.0000 0.780757 0.000 1.000 0.000
#> GSM152987 1 0.2945 0.878760 0.908 0.088 0.004
#> GSM152988 2 0.1163 0.782148 0.000 0.972 0.028
#> GSM152989 2 0.6111 0.174826 0.396 0.604 0.000
#> GSM152990 3 0.1643 0.657038 0.000 0.044 0.956
#> GSM152991 3 0.2711 0.675620 0.000 0.088 0.912
#> GSM187524 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM187525 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM187526 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM187527 1 0.5988 0.434471 0.632 0.368 0.000
#> GSM152856 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152857 2 0.8128 0.016718 0.440 0.492 0.068
#> GSM152858 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152859 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152860 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152861 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152862 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152863 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152864 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152866 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152867 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152870 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152871 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152873 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152874 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152875 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152876 1 0.4121 0.793598 0.832 0.168 0.000
#> GSM152877 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152878 1 0.2711 0.893653 0.912 0.088 0.000
#> GSM152879 1 0.0000 0.972228 1.000 0.000 0.000
#> GSM152880 1 0.0000 0.972228 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.4972 0.6866 0.000 0.544 0.000 0.456
#> GSM152805 2 0.1584 0.6937 0.000 0.952 0.012 0.036
#> GSM152806 2 0.1297 0.6896 0.000 0.964 0.016 0.020
#> GSM152807 2 0.6273 0.6758 0.000 0.488 0.056 0.456
#> GSM152808 2 0.0779 0.6845 0.000 0.980 0.016 0.004
#> GSM152809 4 0.5624 -0.3454 0.000 0.280 0.052 0.668
#> GSM152810 2 0.7505 -0.0161 0.000 0.476 0.200 0.324
#> GSM152811 2 0.2589 0.6604 0.000 0.912 0.044 0.044
#> GSM152812 2 0.4972 0.6866 0.000 0.544 0.000 0.456
#> GSM152813 2 0.4972 0.6866 0.000 0.544 0.000 0.456
#> GSM152814 2 0.5493 0.6878 0.000 0.528 0.016 0.456
#> GSM152815 2 0.6273 0.6720 0.000 0.488 0.056 0.456
#> GSM152816 2 0.1792 0.6983 0.000 0.932 0.000 0.068
#> GSM152817 2 0.2469 0.6736 0.000 0.892 0.108 0.000
#> GSM152818 2 0.0592 0.6823 0.000 0.984 0.016 0.000
#> GSM152819 2 0.4431 0.7263 0.000 0.696 0.000 0.304
#> GSM152820 2 0.1890 0.7064 0.000 0.936 0.008 0.056
#> GSM152821 2 0.5850 0.6806 0.000 0.512 0.032 0.456
#> GSM153115 4 0.1867 0.6141 0.000 0.000 0.072 0.928
#> GSM153116 2 0.4274 0.6996 0.000 0.820 0.108 0.072
#> GSM153117 2 0.6249 0.7015 0.000 0.592 0.072 0.336
#> GSM153118 2 0.5257 0.6916 0.000 0.548 0.008 0.444
#> GSM153119 2 0.2831 0.6725 0.000 0.876 0.120 0.004
#> GSM153120 4 0.6075 0.7348 0.028 0.008 0.476 0.488
#> GSM153121 2 0.3533 0.6704 0.000 0.864 0.056 0.080
#> GSM153122 2 0.2675 0.6557 0.000 0.908 0.044 0.048
#> GSM153123 2 0.4941 0.6953 0.000 0.564 0.000 0.436
#> GSM153124 2 0.7192 0.5874 0.000 0.472 0.140 0.388
#> GSM153125 4 0.4632 0.7360 0.000 0.004 0.308 0.688
#> GSM153126 4 0.6206 0.4840 0.000 0.404 0.056 0.540
#> GSM153127 2 0.6911 0.6747 0.000 0.540 0.124 0.336
#> GSM153128 2 0.4992 0.7138 0.000 0.772 0.096 0.132
#> GSM153129 2 0.1913 0.6902 0.000 0.940 0.040 0.020
#> GSM153130 2 0.0000 0.6854 0.000 1.000 0.000 0.000
#> GSM153131 2 0.2773 0.6778 0.000 0.880 0.004 0.116
#> GSM153132 2 0.1211 0.6916 0.000 0.960 0.040 0.000
#> GSM153133 2 0.6993 0.6745 0.000 0.512 0.124 0.364
#> GSM153134 2 0.4164 0.7255 0.000 0.736 0.000 0.264
#> GSM153135 2 0.6901 0.6690 0.000 0.488 0.108 0.404
#> GSM153136 4 0.4697 0.7508 0.000 0.000 0.356 0.644
#> GSM153137 2 0.5581 0.6873 0.000 0.532 0.020 0.448
#> GSM153138 2 0.4961 0.6895 0.000 0.552 0.000 0.448
#> GSM153139 2 0.1940 0.6991 0.000 0.924 0.000 0.076
#> GSM153140 2 0.4972 0.6866 0.000 0.544 0.000 0.456
#> GSM153141 2 0.5143 0.6867 0.000 0.540 0.004 0.456
#> GSM153142 2 0.1302 0.6808 0.000 0.956 0.044 0.000
#> GSM153143 2 0.7369 0.6449 0.000 0.496 0.180 0.324
#> GSM153144 4 0.4720 -0.1718 0.000 0.264 0.016 0.720
#> GSM153145 2 0.0592 0.6823 0.000 0.984 0.016 0.000
#> GSM153146 2 0.4967 0.6879 0.000 0.548 0.000 0.452
#> GSM153147 4 0.7554 0.2572 0.000 0.316 0.212 0.472
#> GSM153148 2 0.5682 0.6831 0.000 0.520 0.024 0.456
#> GSM153149 2 0.4955 0.6907 0.000 0.556 0.000 0.444
#> GSM153150 4 0.4790 0.7298 0.000 0.000 0.380 0.620
#> GSM153151 2 0.5949 0.7109 0.000 0.644 0.068 0.288
#> GSM153152 2 0.6808 0.6627 0.000 0.572 0.128 0.300
#> GSM153153 2 0.6809 0.6808 0.000 0.532 0.108 0.360
#> GSM153154 2 0.4352 0.6038 0.000 0.816 0.104 0.080
#> GSM153155 2 0.6683 0.6776 0.000 0.496 0.088 0.416
#> GSM153156 2 0.0592 0.6902 0.000 0.984 0.000 0.016
#> GSM153157 2 0.0000 0.6854 0.000 1.000 0.000 0.000
#> GSM153158 2 0.5533 0.7236 0.000 0.708 0.072 0.220
#> GSM153159 2 0.2198 0.6828 0.000 0.920 0.072 0.008
#> GSM153160 2 0.5623 0.1837 0.000 0.660 0.048 0.292
#> GSM153161 2 0.6998 0.6662 0.000 0.468 0.116 0.416
#> GSM153162 4 0.4879 0.6553 0.000 0.128 0.092 0.780
#> GSM153163 2 0.1637 0.6979 0.000 0.940 0.000 0.060
#> GSM153164 2 0.5937 0.7116 0.000 0.608 0.052 0.340
#> GSM153165 2 0.1716 0.6975 0.000 0.936 0.000 0.064
#> GSM153166 2 0.3907 0.7225 0.000 0.768 0.000 0.232
#> GSM153167 2 0.3074 0.7175 0.000 0.848 0.000 0.152
#> GSM153168 2 0.0707 0.6824 0.000 0.980 0.020 0.000
#> GSM153169 2 0.0469 0.6890 0.000 0.988 0.000 0.012
#> GSM153170 2 0.0376 0.6867 0.000 0.992 0.004 0.004
#> GSM153171 4 0.4331 0.7409 0.000 0.000 0.288 0.712
#> GSM153172 2 0.4972 0.6866 0.000 0.544 0.000 0.456
#> GSM153173 2 0.4633 0.4886 0.000 0.780 0.048 0.172
#> GSM153174 4 0.5184 0.7203 0.000 0.056 0.212 0.732
#> GSM153175 4 0.5320 0.7463 0.000 0.012 0.416 0.572
#> GSM153176 4 0.7250 0.6460 0.000 0.220 0.236 0.544
#> GSM153177 2 0.5367 0.7228 0.000 0.664 0.032 0.304
#> GSM152931 4 0.4817 0.7494 0.000 0.000 0.388 0.612
#> GSM152932 2 0.5464 0.7229 0.000 0.716 0.072 0.212
#> GSM152933 2 0.4872 0.7182 0.000 0.640 0.004 0.356
#> GSM152934 4 0.5853 0.7403 0.000 0.032 0.460 0.508
#> GSM152935 2 0.5564 0.6946 0.000 0.544 0.020 0.436
#> GSM152936 4 0.4790 0.7458 0.000 0.000 0.380 0.620
#> GSM152937 2 0.4644 0.6360 0.000 0.748 0.228 0.024
#> GSM152938 2 0.3946 0.6382 0.000 0.812 0.020 0.168
#> GSM152939 4 0.4356 0.7419 0.000 0.000 0.292 0.708
#> GSM152940 4 0.5155 0.7455 0.000 0.004 0.468 0.528
#> GSM152941 3 0.4883 0.3999 0.288 0.000 0.696 0.016
#> GSM152942 4 0.7274 0.6332 0.000 0.240 0.220 0.540
#> GSM152943 2 0.7504 0.5785 0.000 0.464 0.192 0.344
#> GSM152944 2 0.1042 0.6837 0.000 0.972 0.020 0.008
#> GSM152945 2 0.7189 0.6599 0.000 0.532 0.168 0.300
#> GSM152946 2 0.6268 0.6571 0.000 0.496 0.056 0.448
#> GSM152947 4 0.5088 0.7412 0.004 0.000 0.424 0.572
#> GSM152948 2 0.4972 0.6866 0.000 0.544 0.000 0.456
#> GSM152949 2 0.6554 -0.1918 0.000 0.540 0.084 0.376
#> GSM152950 2 0.6974 -0.2388 0.000 0.488 0.116 0.396
#> GSM152951 4 0.6310 -0.6349 0.000 0.428 0.060 0.512
#> GSM152952 2 0.6949 0.6691 0.000 0.480 0.112 0.408
#> GSM152953 2 0.4972 0.6866 0.000 0.544 0.000 0.456
#> GSM152954 4 0.7429 0.6580 0.000 0.176 0.360 0.464
#> GSM152955 2 0.4804 0.6006 0.000 0.708 0.276 0.016
#> GSM152956 2 0.4972 0.6866 0.000 0.544 0.000 0.456
#> GSM152957 4 0.3873 0.7179 0.000 0.000 0.228 0.772
#> GSM152958 4 0.5088 0.7413 0.004 0.000 0.424 0.572
#> GSM152959 4 0.4989 0.7448 0.000 0.000 0.472 0.528
#> GSM152960 4 0.7687 0.2369 0.000 0.240 0.312 0.448
#> GSM152961 4 0.5823 0.7247 0.044 0.000 0.348 0.608
#> GSM152962 2 0.7091 0.6405 0.000 0.564 0.188 0.248
#> GSM152963 2 0.6003 0.6829 0.000 0.504 0.040 0.456
#> GSM152964 2 0.6537 0.2798 0.000 0.500 0.424 0.076
#> GSM152965 2 0.6837 0.6772 0.000 0.544 0.116 0.340
#> GSM152966 4 0.4933 0.7433 0.000 0.000 0.432 0.568
#> GSM152967 4 0.3984 0.5831 0.000 0.040 0.132 0.828
#> GSM152968 2 0.0469 0.6893 0.000 0.988 0.000 0.012
#> GSM152969 3 0.7728 -0.6311 0.000 0.232 0.416 0.352
#> GSM152970 4 0.7024 0.7347 0.032 0.052 0.408 0.508
#> GSM152971 4 0.4948 0.7445 0.000 0.000 0.440 0.560
#> GSM152972 4 0.4994 0.7431 0.000 0.000 0.480 0.520
#> GSM152973 4 0.7182 0.6237 0.000 0.248 0.200 0.552
#> GSM152974 2 0.6347 0.6881 0.000 0.524 0.064 0.412
#> GSM152975 4 0.6371 0.6371 0.000 0.092 0.300 0.608
#> GSM152976 4 0.4456 0.7393 0.000 0.004 0.280 0.716
#> GSM152977 4 0.7654 0.6724 0.000 0.216 0.352 0.432
#> GSM152978 4 0.7210 0.5841 0.000 0.148 0.360 0.492
#> GSM152979 2 0.0937 0.6888 0.000 0.976 0.012 0.012
#> GSM152980 2 0.6876 0.6591 0.000 0.572 0.140 0.288
#> GSM152981 2 0.2675 0.6825 0.000 0.892 0.100 0.008
#> GSM152982 4 0.5320 0.7459 0.000 0.012 0.416 0.572
#> GSM152983 4 0.4907 0.7464 0.000 0.000 0.420 0.580
#> GSM152984 4 0.4990 0.7071 0.000 0.060 0.184 0.756
#> GSM152985 4 0.6954 0.6337 0.116 0.000 0.384 0.500
#> GSM152986 4 0.4925 0.7455 0.000 0.000 0.428 0.572
#> GSM152987 3 0.5291 0.4225 0.324 0.000 0.652 0.024
#> GSM152988 4 0.4511 0.7376 0.000 0.008 0.268 0.724
#> GSM152989 4 0.6367 0.6789 0.068 0.000 0.392 0.540
#> GSM152990 2 0.2586 0.6580 0.000 0.912 0.040 0.048
#> GSM152991 2 0.3497 0.6799 0.000 0.852 0.124 0.024
#> GSM187524 3 0.4977 0.4643 0.460 0.000 0.540 0.000
#> GSM187525 3 0.4730 0.4950 0.364 0.000 0.636 0.000
#> GSM187526 3 0.4985 0.5929 0.468 0.000 0.532 0.000
#> GSM187527 1 0.2805 0.5329 0.888 0.000 0.100 0.012
#> GSM152856 1 0.0000 0.6604 1.000 0.000 0.000 0.000
#> GSM152857 1 0.4429 0.4313 0.804 0.008 0.156 0.032
#> GSM152858 3 0.5000 0.5724 0.500 0.000 0.500 0.000
#> GSM152859 3 0.4999 0.5852 0.492 0.000 0.508 0.000
#> GSM152860 3 0.4998 0.5896 0.488 0.000 0.512 0.000
#> GSM152861 1 0.5000 -0.6244 0.500 0.000 0.500 0.000
#> GSM152862 3 0.4994 0.5941 0.480 0.000 0.520 0.000
#> GSM152863 1 0.4961 -0.5138 0.552 0.000 0.448 0.000
#> GSM152864 1 0.5000 -0.6244 0.500 0.000 0.500 0.000
#> GSM152865 3 0.5000 0.5724 0.500 0.000 0.500 0.000
#> GSM152866 1 0.0000 0.6604 1.000 0.000 0.000 0.000
#> GSM152867 1 0.5000 -0.6244 0.500 0.000 0.500 0.000
#> GSM152868 3 0.5000 0.5724 0.500 0.000 0.500 0.000
#> GSM152869 1 0.5000 -0.6244 0.500 0.000 0.500 0.000
#> GSM152870 3 0.4989 0.5946 0.472 0.000 0.528 0.000
#> GSM152871 3 0.5000 0.5724 0.500 0.000 0.500 0.000
#> GSM152872 3 0.5000 0.5724 0.500 0.000 0.500 0.000
#> GSM152873 1 0.0000 0.6604 1.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.6604 1.000 0.000 0.000 0.000
#> GSM152875 1 0.0000 0.6604 1.000 0.000 0.000 0.000
#> GSM152876 1 0.1743 0.6003 0.940 0.000 0.056 0.004
#> GSM152877 1 0.0000 0.6604 1.000 0.000 0.000 0.000
#> GSM152878 1 0.0895 0.6402 0.976 0.000 0.020 0.004
#> GSM152879 1 0.0000 0.6604 1.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.6604 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.4268 0.7773 0.000 0.556 0.444 0.000 0.000
#> GSM152805 3 0.3994 0.5713 0.000 0.188 0.772 0.000 0.040
#> GSM152806 3 0.4938 0.5415 0.000 0.312 0.640 0.000 0.048
#> GSM152807 2 0.4074 0.7815 0.000 0.636 0.364 0.000 0.000
#> GSM152808 3 0.5182 0.5383 0.000 0.300 0.632 0.000 0.068
#> GSM152809 2 0.5799 0.6033 0.000 0.612 0.220 0.168 0.000
#> GSM152810 3 0.7188 0.0279 0.000 0.204 0.416 0.352 0.028
#> GSM152811 3 0.4737 0.5697 0.000 0.128 0.772 0.048 0.052
#> GSM152812 2 0.4256 0.7807 0.000 0.564 0.436 0.000 0.000
#> GSM152813 2 0.4268 0.7773 0.000 0.556 0.444 0.000 0.000
#> GSM152814 2 0.3752 0.6784 0.000 0.708 0.292 0.000 0.000
#> GSM152815 2 0.4150 0.7777 0.000 0.612 0.388 0.000 0.000
#> GSM152816 3 0.1341 0.5322 0.000 0.056 0.944 0.000 0.000
#> GSM152817 3 0.6064 0.5244 0.000 0.316 0.580 0.028 0.076
#> GSM152818 3 0.5126 0.5387 0.000 0.300 0.636 0.000 0.064
#> GSM152819 3 0.4682 -0.4046 0.000 0.356 0.620 0.000 0.024
#> GSM152820 3 0.2291 0.5000 0.000 0.072 0.908 0.008 0.012
#> GSM152821 2 0.4201 0.7851 0.000 0.592 0.408 0.000 0.000
#> GSM153115 4 0.4283 0.3831 0.000 0.456 0.000 0.544 0.000
#> GSM153116 3 0.5685 0.4568 0.000 0.316 0.608 0.040 0.036
#> GSM153117 2 0.5538 0.4957 0.000 0.616 0.316 0.040 0.028
#> GSM153118 2 0.4610 0.7742 0.000 0.556 0.432 0.000 0.012
#> GSM153119 3 0.5409 0.5362 0.000 0.260 0.664 0.036 0.040
#> GSM153120 4 0.2804 0.7578 0.000 0.068 0.004 0.884 0.044
#> GSM153121 3 0.4862 0.5645 0.000 0.228 0.712 0.044 0.016
#> GSM153122 3 0.3639 0.5719 0.000 0.100 0.824 0.076 0.000
#> GSM153123 2 0.4291 0.7644 0.000 0.536 0.464 0.000 0.000
#> GSM153124 2 0.6596 0.6011 0.000 0.416 0.372 0.212 0.000
#> GSM153125 4 0.2930 0.7523 0.000 0.164 0.004 0.832 0.000
#> GSM153126 3 0.4305 -0.1172 0.000 0.000 0.512 0.488 0.000
#> GSM153127 2 0.5681 0.6315 0.000 0.576 0.356 0.040 0.028
#> GSM153128 3 0.4961 0.2176 0.000 0.208 0.720 0.048 0.024
#> GSM153129 3 0.1582 0.5506 0.000 0.028 0.944 0.028 0.000
#> GSM153130 3 0.0000 0.5697 0.000 0.000 1.000 0.000 0.000
#> GSM153131 3 0.2588 0.5494 0.000 0.060 0.892 0.048 0.000
#> GSM153132 3 0.1989 0.5631 0.000 0.020 0.932 0.032 0.016
#> GSM153133 2 0.5153 0.5730 0.000 0.680 0.256 0.040 0.024
#> GSM153134 3 0.3816 -0.1684 0.000 0.304 0.696 0.000 0.000
#> GSM153135 2 0.5329 0.7581 0.000 0.564 0.388 0.040 0.008
#> GSM153136 4 0.2424 0.7784 0.000 0.132 0.000 0.868 0.000
#> GSM153137 2 0.4510 0.7835 0.000 0.560 0.432 0.008 0.000
#> GSM153138 2 0.4528 0.7774 0.000 0.548 0.444 0.000 0.008
#> GSM153139 3 0.1478 0.5227 0.000 0.064 0.936 0.000 0.000
#> GSM153140 2 0.4268 0.7773 0.000 0.556 0.444 0.000 0.000
#> GSM153141 2 0.4262 0.7797 0.000 0.560 0.440 0.000 0.000
#> GSM153142 3 0.5219 0.5478 0.000 0.288 0.644 0.004 0.064
#> GSM153143 2 0.6107 0.4308 0.000 0.616 0.232 0.132 0.020
#> GSM153144 2 0.6307 0.5150 0.000 0.532 0.224 0.244 0.000
#> GSM153145 3 0.5182 0.5383 0.000 0.300 0.632 0.000 0.068
#> GSM153146 2 0.4632 0.7768 0.000 0.540 0.448 0.000 0.012
#> GSM153147 4 0.6438 0.2407 0.000 0.220 0.280 0.500 0.000
#> GSM153148 2 0.4227 0.7839 0.000 0.580 0.420 0.000 0.000
#> GSM153149 2 0.4528 0.7787 0.000 0.548 0.444 0.000 0.008
#> GSM153150 4 0.2886 0.7624 0.000 0.148 0.000 0.844 0.008
#> GSM153151 3 0.6145 -0.6366 0.000 0.368 0.532 0.076 0.024
#> GSM153152 2 0.5997 0.3128 0.000 0.588 0.312 0.072 0.028
#> GSM153153 2 0.5736 0.7165 0.000 0.520 0.416 0.040 0.024
#> GSM153154 3 0.5373 0.5469 0.000 0.244 0.676 0.048 0.032
#> GSM153155 2 0.4895 0.7684 0.000 0.596 0.376 0.024 0.004
#> GSM153156 3 0.0510 0.5630 0.000 0.016 0.984 0.000 0.000
#> GSM153157 3 0.0807 0.5748 0.000 0.012 0.976 0.000 0.012
#> GSM153158 2 0.5771 0.0823 0.000 0.476 0.460 0.040 0.024
#> GSM153159 3 0.4737 0.5587 0.000 0.216 0.728 0.028 0.028
#> GSM153160 3 0.3661 0.4902 0.000 0.000 0.724 0.276 0.000
#> GSM153161 2 0.5030 0.7499 0.000 0.624 0.336 0.032 0.008
#> GSM153162 4 0.5974 0.4981 0.000 0.320 0.132 0.548 0.000
#> GSM153163 3 0.1410 0.5424 0.000 0.060 0.940 0.000 0.000
#> GSM153164 2 0.5681 0.4388 0.000 0.576 0.356 0.040 0.028
#> GSM153165 3 0.1270 0.5356 0.000 0.052 0.948 0.000 0.000
#> GSM153166 3 0.3730 -0.0619 0.000 0.288 0.712 0.000 0.000
#> GSM153167 3 0.2966 0.2874 0.000 0.184 0.816 0.000 0.000
#> GSM153168 3 0.5182 0.5383 0.000 0.300 0.632 0.000 0.068
#> GSM153169 3 0.0404 0.5648 0.000 0.012 0.988 0.000 0.000
#> GSM153170 3 0.0324 0.5691 0.000 0.004 0.992 0.004 0.000
#> GSM153171 4 0.2891 0.7603 0.000 0.176 0.000 0.824 0.000
#> GSM153172 2 0.4268 0.7773 0.000 0.556 0.444 0.000 0.000
#> GSM153173 3 0.4219 0.5679 0.000 0.072 0.772 0.156 0.000
#> GSM153174 4 0.4612 0.7181 0.000 0.196 0.056 0.740 0.008
#> GSM153175 4 0.0566 0.7781 0.000 0.012 0.004 0.984 0.000
#> GSM153176 4 0.3242 0.6547 0.000 0.000 0.216 0.784 0.000
#> GSM153177 3 0.5338 -0.6325 0.000 0.400 0.556 0.028 0.016
#> GSM152931 4 0.1043 0.7793 0.000 0.040 0.000 0.960 0.000
#> GSM152932 3 0.5322 -0.3544 0.000 0.336 0.612 0.024 0.028
#> GSM152933 3 0.4650 -0.6254 0.000 0.468 0.520 0.000 0.012
#> GSM152934 4 0.2228 0.7715 0.000 0.056 0.020 0.916 0.008
#> GSM152935 2 0.4764 0.7794 0.000 0.548 0.436 0.004 0.012
#> GSM152936 4 0.3093 0.7719 0.000 0.168 0.000 0.824 0.008
#> GSM152937 3 0.5728 0.3039 0.000 0.096 0.660 0.220 0.024
#> GSM152938 3 0.3176 0.5497 0.000 0.080 0.856 0.064 0.000
#> GSM152939 4 0.2516 0.7674 0.000 0.140 0.000 0.860 0.000
#> GSM152940 4 0.1569 0.7745 0.000 0.044 0.004 0.944 0.008
#> GSM152941 1 0.3826 0.6837 0.752 0.008 0.000 0.236 0.004
#> GSM152942 4 0.3508 0.6094 0.000 0.000 0.252 0.748 0.000
#> GSM152943 2 0.6835 0.5260 0.000 0.380 0.376 0.240 0.004
#> GSM152944 3 0.3648 0.5700 0.000 0.188 0.792 0.004 0.016
#> GSM152945 2 0.6032 0.4375 0.000 0.624 0.256 0.084 0.036
#> GSM152946 2 0.5723 0.7443 0.000 0.520 0.392 0.088 0.000
#> GSM152947 4 0.0000 0.7720 0.000 0.000 0.000 1.000 0.000
#> GSM152948 2 0.4268 0.7773 0.000 0.556 0.444 0.000 0.000
#> GSM152949 3 0.6108 0.3864 0.000 0.224 0.568 0.208 0.000
#> GSM152950 3 0.6415 0.4339 0.000 0.252 0.548 0.192 0.008
#> GSM152951 2 0.4584 0.7533 0.000 0.660 0.312 0.028 0.000
#> GSM152952 2 0.5119 0.7607 0.000 0.592 0.360 0.048 0.000
#> GSM152953 2 0.4268 0.7773 0.000 0.556 0.444 0.000 0.000
#> GSM152954 4 0.4059 0.6955 0.000 0.052 0.172 0.776 0.000
#> GSM152955 3 0.5547 0.2014 0.000 0.052 0.632 0.292 0.024
#> GSM152956 2 0.4268 0.7773 0.000 0.556 0.444 0.000 0.000
#> GSM152957 4 0.3274 0.7340 0.000 0.220 0.000 0.780 0.000
#> GSM152958 4 0.0000 0.7720 0.000 0.000 0.000 1.000 0.000
#> GSM152959 4 0.1357 0.7736 0.000 0.048 0.000 0.948 0.004
#> GSM152960 4 0.6566 0.2083 0.000 0.288 0.192 0.512 0.008
#> GSM152961 4 0.1943 0.7685 0.020 0.056 0.000 0.924 0.000
#> GSM152962 3 0.7225 -0.4365 0.000 0.304 0.448 0.216 0.032
#> GSM152963 2 0.3999 0.7644 0.000 0.656 0.344 0.000 0.000
#> GSM152964 4 0.7133 0.0501 0.000 0.260 0.260 0.456 0.024
#> GSM152965 2 0.5805 0.6905 0.000 0.520 0.412 0.040 0.028
#> GSM152966 4 0.0162 0.7733 0.000 0.004 0.000 0.996 0.000
#> GSM152967 4 0.5368 0.3111 0.000 0.476 0.036 0.480 0.008
#> GSM152968 3 0.0771 0.5703 0.000 0.020 0.976 0.000 0.004
#> GSM152969 4 0.3724 0.6528 0.000 0.020 0.204 0.776 0.000
#> GSM152970 4 0.3685 0.7642 0.052 0.048 0.052 0.848 0.000
#> GSM152971 4 0.0404 0.7746 0.000 0.012 0.000 0.988 0.000
#> GSM152972 4 0.1697 0.7716 0.000 0.060 0.000 0.932 0.008
#> GSM152973 4 0.3809 0.6082 0.000 0.008 0.256 0.736 0.000
#> GSM152974 2 0.4947 0.7757 0.000 0.576 0.396 0.024 0.004
#> GSM152975 4 0.5772 0.5605 0.000 0.284 0.100 0.608 0.008
#> GSM152976 4 0.3010 0.7567 0.000 0.172 0.000 0.824 0.004
#> GSM152977 4 0.3328 0.7273 0.000 0.004 0.176 0.812 0.008
#> GSM152978 4 0.5815 0.5395 0.000 0.208 0.148 0.636 0.008
#> GSM152979 3 0.0451 0.5696 0.000 0.004 0.988 0.008 0.000
#> GSM152980 3 0.6214 -0.5777 0.000 0.380 0.476 0.144 0.000
#> GSM152981 3 0.5558 0.5356 0.000 0.232 0.672 0.036 0.060
#> GSM152982 4 0.0451 0.7768 0.000 0.004 0.008 0.988 0.000
#> GSM152983 4 0.0290 0.7767 0.000 0.008 0.000 0.992 0.000
#> GSM152984 4 0.4872 0.6943 0.000 0.248 0.056 0.692 0.004
#> GSM152985 4 0.1952 0.7392 0.084 0.004 0.000 0.912 0.000
#> GSM152986 4 0.0404 0.7777 0.000 0.012 0.000 0.988 0.000
#> GSM152987 1 0.4690 0.6391 0.708 0.048 0.000 0.240 0.004
#> GSM152988 4 0.2929 0.7650 0.000 0.152 0.008 0.840 0.000
#> GSM152989 4 0.1270 0.7519 0.052 0.000 0.000 0.948 0.000
#> GSM152990 3 0.1768 0.5714 0.000 0.004 0.924 0.072 0.000
#> GSM152991 3 0.5519 0.5088 0.000 0.280 0.644 0.040 0.036
#> GSM187524 1 0.5752 0.6278 0.668 0.020 0.000 0.140 0.172
#> GSM187525 1 0.2900 0.8314 0.864 0.028 0.000 0.108 0.000
#> GSM187526 1 0.1792 0.8478 0.916 0.000 0.000 0.084 0.000
#> GSM187527 5 0.1671 0.9938 0.076 0.000 0.000 0.000 0.924
#> GSM152856 5 0.1671 0.9938 0.076 0.000 0.000 0.000 0.924
#> GSM152857 5 0.1469 0.9478 0.036 0.000 0.000 0.016 0.948
#> GSM152858 1 0.2136 0.8794 0.904 0.088 0.000 0.000 0.008
#> GSM152859 1 0.1851 0.8824 0.912 0.088 0.000 0.000 0.000
#> GSM152860 1 0.1851 0.8824 0.912 0.088 0.000 0.000 0.000
#> GSM152861 1 0.0000 0.8828 1.000 0.000 0.000 0.000 0.000
#> GSM152862 1 0.1851 0.8824 0.912 0.088 0.000 0.000 0.000
#> GSM152863 1 0.2127 0.8298 0.892 0.000 0.000 0.000 0.108
#> GSM152864 1 0.0880 0.8798 0.968 0.000 0.000 0.000 0.032
#> GSM152865 1 0.0963 0.8787 0.964 0.000 0.000 0.000 0.036
#> GSM152866 5 0.1671 0.9938 0.076 0.000 0.000 0.000 0.924
#> GSM152867 1 0.1121 0.8759 0.956 0.000 0.000 0.000 0.044
#> GSM152868 1 0.1121 0.8759 0.956 0.000 0.000 0.000 0.044
#> GSM152869 1 0.0510 0.8823 0.984 0.000 0.000 0.000 0.016
#> GSM152870 1 0.1851 0.8824 0.912 0.088 0.000 0.000 0.000
#> GSM152871 1 0.1851 0.8824 0.912 0.088 0.000 0.000 0.000
#> GSM152872 1 0.1851 0.8824 0.912 0.088 0.000 0.000 0.000
#> GSM152873 5 0.1671 0.9938 0.076 0.000 0.000 0.000 0.924
#> GSM152874 5 0.1671 0.9938 0.076 0.000 0.000 0.000 0.924
#> GSM152875 5 0.1671 0.9938 0.076 0.000 0.000 0.000 0.924
#> GSM152876 5 0.1768 0.9897 0.072 0.000 0.000 0.004 0.924
#> GSM152877 5 0.1671 0.9938 0.076 0.000 0.000 0.000 0.924
#> GSM152878 5 0.1768 0.9897 0.072 0.000 0.000 0.004 0.924
#> GSM152879 5 0.1671 0.9938 0.076 0.000 0.000 0.000 0.924
#> GSM152880 5 0.1671 0.9938 0.076 0.000 0.000 0.000 0.924
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.0146 0.7065 0.000 0.996 0.000 0.004 0.000 0.000
#> GSM152805 3 0.2800 0.5384 0.000 0.100 0.860 0.000 0.004 0.036
#> GSM152806 3 0.2871 0.4465 0.000 0.000 0.804 0.000 0.004 0.192
#> GSM152807 2 0.1829 0.7096 0.000 0.920 0.024 0.000 0.000 0.056
#> GSM152808 3 0.3489 0.4260 0.000 0.000 0.708 0.000 0.004 0.288
#> GSM152809 2 0.3495 0.6273 0.000 0.808 0.004 0.128 0.000 0.060
#> GSM152810 4 0.7625 0.0527 0.000 0.212 0.280 0.316 0.000 0.192
#> GSM152811 3 0.4069 0.5414 0.000 0.112 0.788 0.020 0.004 0.076
#> GSM152812 2 0.0146 0.7070 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM152813 2 0.0000 0.7056 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152814 2 0.1957 0.6762 0.000 0.888 0.112 0.000 0.000 0.000
#> GSM152815 2 0.1327 0.7068 0.000 0.936 0.000 0.000 0.000 0.064
#> GSM152816 3 0.3747 0.5494 0.000 0.396 0.604 0.000 0.000 0.000
#> GSM152817 3 0.3619 0.4128 0.000 0.000 0.680 0.000 0.004 0.316
#> GSM152818 3 0.3314 0.4377 0.000 0.000 0.740 0.000 0.004 0.256
#> GSM152819 2 0.4881 0.3847 0.000 0.656 0.136 0.000 0.000 0.208
#> GSM152820 3 0.4927 0.4379 0.000 0.452 0.496 0.008 0.000 0.044
#> GSM152821 2 0.1124 0.7130 0.000 0.956 0.008 0.000 0.000 0.036
#> GSM153115 2 0.3868 -0.2440 0.000 0.504 0.000 0.496 0.000 0.000
#> GSM153116 3 0.6159 0.3672 0.000 0.256 0.404 0.004 0.000 0.336
#> GSM153117 2 0.5657 0.3786 0.000 0.556 0.160 0.008 0.000 0.276
#> GSM153118 2 0.2581 0.6756 0.000 0.860 0.020 0.000 0.000 0.120
#> GSM153119 3 0.5952 0.4478 0.000 0.172 0.460 0.008 0.000 0.360
#> GSM153120 4 0.2764 0.7396 0.000 0.000 0.008 0.864 0.028 0.100
#> GSM153121 3 0.6503 0.4914 0.000 0.204 0.496 0.048 0.000 0.252
#> GSM153122 3 0.4150 0.5704 0.000 0.204 0.732 0.060 0.000 0.004
#> GSM153123 2 0.1007 0.6951 0.000 0.956 0.044 0.000 0.000 0.000
#> GSM153124 2 0.3265 0.5946 0.000 0.748 0.004 0.248 0.000 0.000
#> GSM153125 4 0.2597 0.7221 0.000 0.176 0.000 0.824 0.000 0.000
#> GSM153126 3 0.3782 0.1123 0.000 0.000 0.588 0.412 0.000 0.000
#> GSM153127 2 0.4698 0.5916 0.000 0.676 0.076 0.008 0.000 0.240
#> GSM153128 2 0.6161 -0.0614 0.000 0.476 0.264 0.012 0.000 0.248
#> GSM153129 3 0.4168 0.5313 0.000 0.400 0.584 0.016 0.000 0.000
#> GSM153130 3 0.3706 0.5631 0.000 0.380 0.620 0.000 0.000 0.000
#> GSM153131 3 0.4420 0.5643 0.000 0.360 0.604 0.036 0.000 0.000
#> GSM153132 3 0.5623 0.5139 0.000 0.372 0.500 0.008 0.000 0.120
#> GSM153133 2 0.5393 0.4910 0.000 0.592 0.128 0.008 0.000 0.272
#> GSM153134 2 0.3499 0.2384 0.000 0.680 0.320 0.000 0.000 0.000
#> GSM153135 2 0.2070 0.7003 0.000 0.892 0.000 0.008 0.000 0.100
#> GSM153136 4 0.3150 0.7594 0.000 0.104 0.000 0.832 0.000 0.064
#> GSM153137 2 0.0692 0.7118 0.000 0.976 0.000 0.004 0.000 0.020
#> GSM153138 2 0.0405 0.7049 0.000 0.988 0.008 0.000 0.000 0.004
#> GSM153139 3 0.3747 0.5485 0.000 0.396 0.604 0.000 0.000 0.000
#> GSM153140 2 0.0146 0.7049 0.000 0.996 0.004 0.000 0.000 0.000
#> GSM153141 2 0.0146 0.7072 0.000 0.996 0.000 0.000 0.000 0.004
#> GSM153142 3 0.4602 0.5117 0.000 0.068 0.668 0.004 0.000 0.260
#> GSM153143 2 0.6716 0.3413 0.000 0.468 0.136 0.088 0.000 0.308
#> GSM153144 2 0.2823 0.5748 0.000 0.796 0.000 0.204 0.000 0.000
#> GSM153145 3 0.3489 0.4260 0.000 0.000 0.708 0.000 0.004 0.288
#> GSM153146 2 0.1584 0.7015 0.000 0.928 0.008 0.000 0.000 0.064
#> GSM153147 4 0.5350 0.2522 0.000 0.424 0.060 0.496 0.000 0.020
#> GSM153148 2 0.0632 0.7106 0.000 0.976 0.000 0.000 0.000 0.024
#> GSM153149 2 0.2070 0.6923 0.000 0.896 0.012 0.000 0.000 0.092
#> GSM153150 4 0.3518 0.7276 0.000 0.104 0.000 0.804 0.000 0.092
#> GSM153151 2 0.4686 0.6078 0.000 0.740 0.052 0.076 0.000 0.132
#> GSM153152 2 0.6414 0.2945 0.000 0.448 0.172 0.036 0.000 0.344
#> GSM153153 2 0.4105 0.6320 0.000 0.720 0.036 0.008 0.000 0.236
#> GSM153154 3 0.6113 0.4621 0.000 0.176 0.464 0.016 0.000 0.344
#> GSM153155 2 0.2009 0.7065 0.000 0.904 0.008 0.004 0.000 0.084
#> GSM153156 3 0.3945 0.5635 0.000 0.380 0.612 0.000 0.000 0.008
#> GSM153157 3 0.4482 0.5718 0.000 0.360 0.600 0.000 0.000 0.040
#> GSM153158 2 0.6128 0.1171 0.000 0.464 0.260 0.008 0.000 0.268
#> GSM153159 3 0.5935 0.4816 0.000 0.212 0.484 0.004 0.000 0.300
#> GSM153160 3 0.5231 0.5179 0.000 0.168 0.608 0.224 0.000 0.000
#> GSM153161 2 0.2863 0.6956 0.000 0.860 0.036 0.008 0.000 0.096
#> GSM153162 4 0.5805 0.4196 0.000 0.340 0.112 0.524 0.000 0.024
#> GSM153163 3 0.3737 0.5535 0.000 0.392 0.608 0.000 0.000 0.000
#> GSM153164 2 0.5572 0.3650 0.000 0.580 0.168 0.008 0.000 0.244
#> GSM153165 3 0.3737 0.5535 0.000 0.392 0.608 0.000 0.000 0.000
#> GSM153166 2 0.3547 0.1784 0.000 0.668 0.332 0.000 0.000 0.000
#> GSM153167 2 0.3860 -0.2589 0.000 0.528 0.472 0.000 0.000 0.000
#> GSM153168 3 0.3489 0.4260 0.000 0.000 0.708 0.000 0.004 0.288
#> GSM153169 3 0.3706 0.5631 0.000 0.380 0.620 0.000 0.000 0.000
#> GSM153170 3 0.3706 0.5631 0.000 0.380 0.620 0.000 0.000 0.000
#> GSM153171 4 0.2416 0.7475 0.000 0.156 0.000 0.844 0.000 0.000
#> GSM153172 2 0.0000 0.7056 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM153173 3 0.4855 0.5745 0.000 0.204 0.660 0.136 0.000 0.000
#> GSM153174 4 0.4356 0.6763 0.000 0.232 0.032 0.712 0.000 0.024
#> GSM153175 4 0.0717 0.7651 0.000 0.016 0.008 0.976 0.000 0.000
#> GSM153176 4 0.2912 0.6543 0.000 0.000 0.216 0.784 0.000 0.000
#> GSM153177 2 0.3473 0.6075 0.000 0.804 0.144 0.004 0.000 0.048
#> GSM152931 4 0.0632 0.7649 0.000 0.024 0.000 0.976 0.000 0.000
#> GSM152932 2 0.4959 0.4611 0.000 0.656 0.216 0.004 0.000 0.124
#> GSM152933 2 0.3901 0.5941 0.000 0.768 0.096 0.000 0.000 0.136
#> GSM152934 4 0.2212 0.7486 0.000 0.008 0.000 0.880 0.000 0.112
#> GSM152935 2 0.2747 0.6905 0.000 0.860 0.028 0.004 0.000 0.108
#> GSM152936 4 0.3782 0.7378 0.000 0.124 0.000 0.780 0.000 0.096
#> GSM152937 2 0.7483 -0.1732 0.000 0.352 0.276 0.224 0.000 0.148
#> GSM152938 3 0.5161 0.5378 0.000 0.348 0.576 0.056 0.000 0.020
#> GSM152939 4 0.2378 0.7435 0.000 0.152 0.000 0.848 0.000 0.000
#> GSM152940 4 0.1556 0.7571 0.000 0.000 0.000 0.920 0.000 0.080
#> GSM152941 1 0.3650 0.4984 0.716 0.008 0.000 0.272 0.000 0.004
#> GSM152942 4 0.3789 0.5943 0.000 0.000 0.260 0.716 0.000 0.024
#> GSM152943 2 0.4430 0.5247 0.000 0.668 0.004 0.280 0.000 0.048
#> GSM152944 3 0.4985 0.5696 0.000 0.240 0.644 0.004 0.000 0.112
#> GSM152945 2 0.6194 0.3404 0.000 0.476 0.144 0.032 0.000 0.348
#> GSM152946 2 0.2275 0.6925 0.000 0.888 0.008 0.096 0.000 0.008
#> GSM152947 4 0.0000 0.7561 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152948 2 0.0000 0.7056 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152949 3 0.4824 0.4795 0.000 0.020 0.700 0.184 0.000 0.096
#> GSM152950 3 0.6004 0.5042 0.000 0.060 0.600 0.152 0.000 0.188
#> GSM152951 2 0.2784 0.6964 0.000 0.876 0.040 0.020 0.000 0.064
#> GSM152952 2 0.2883 0.7003 0.000 0.864 0.016 0.032 0.000 0.088
#> GSM152953 2 0.0260 0.7041 0.000 0.992 0.008 0.000 0.000 0.000
#> GSM152954 4 0.2913 0.7018 0.000 0.180 0.004 0.812 0.000 0.004
#> GSM152955 2 0.7234 -0.1040 0.000 0.408 0.200 0.272 0.000 0.120
#> GSM152956 2 0.0000 0.7056 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152957 4 0.2883 0.7112 0.000 0.212 0.000 0.788 0.000 0.000
#> GSM152958 4 0.0000 0.7561 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152959 4 0.1501 0.7567 0.000 0.000 0.000 0.924 0.000 0.076
#> GSM152960 4 0.5213 0.1527 0.000 0.420 0.000 0.488 0.000 0.092
#> GSM152961 4 0.1152 0.7646 0.004 0.044 0.000 0.952 0.000 0.000
#> GSM152962 2 0.5683 0.4408 0.000 0.596 0.020 0.212 0.000 0.172
#> GSM152963 2 0.1930 0.7093 0.000 0.916 0.048 0.000 0.000 0.036
#> GSM152964 4 0.7526 -0.1292 0.000 0.204 0.164 0.328 0.000 0.304
#> GSM152965 2 0.4154 0.6224 0.000 0.712 0.036 0.008 0.000 0.244
#> GSM152966 4 0.0458 0.7609 0.000 0.000 0.000 0.984 0.000 0.016
#> GSM152967 2 0.5780 -0.1157 0.000 0.480 0.016 0.388 0.000 0.116
#> GSM152968 3 0.4121 0.5637 0.000 0.380 0.604 0.000 0.000 0.016
#> GSM152969 4 0.2845 0.6927 0.000 0.172 0.004 0.820 0.000 0.004
#> GSM152970 4 0.3127 0.7533 0.044 0.084 0.000 0.852 0.000 0.020
#> GSM152971 4 0.0865 0.7625 0.000 0.000 0.000 0.964 0.000 0.036
#> GSM152972 4 0.1958 0.7503 0.000 0.004 0.000 0.896 0.000 0.100
#> GSM152973 4 0.3337 0.6137 0.000 0.004 0.260 0.736 0.000 0.000
#> GSM152974 2 0.2239 0.7142 0.000 0.900 0.020 0.008 0.000 0.072
#> GSM152975 4 0.5257 0.4918 0.000 0.328 0.000 0.556 0.000 0.116
#> GSM152976 4 0.2631 0.7305 0.000 0.180 0.000 0.820 0.000 0.000
#> GSM152977 4 0.2841 0.7332 0.000 0.092 0.032 0.864 0.000 0.012
#> GSM152978 4 0.5114 0.4938 0.000 0.292 0.004 0.604 0.000 0.100
#> GSM152979 3 0.3706 0.5631 0.000 0.380 0.620 0.000 0.000 0.000
#> GSM152980 2 0.3660 0.5817 0.000 0.780 0.060 0.160 0.000 0.000
#> GSM152981 3 0.6069 0.4354 0.000 0.232 0.440 0.000 0.004 0.324
#> GSM152982 4 0.0405 0.7612 0.000 0.004 0.000 0.988 0.000 0.008
#> GSM152983 4 0.0260 0.7612 0.000 0.008 0.000 0.992 0.000 0.000
#> GSM152984 4 0.4988 0.6412 0.000 0.264 0.068 0.648 0.000 0.020
#> GSM152985 4 0.1616 0.7489 0.048 0.000 0.000 0.932 0.000 0.020
#> GSM152986 4 0.0508 0.7641 0.000 0.012 0.000 0.984 0.000 0.004
#> GSM152987 1 0.4139 0.5484 0.744 0.008 0.000 0.188 0.000 0.060
#> GSM152988 4 0.2669 0.7403 0.000 0.156 0.008 0.836 0.000 0.000
#> GSM152989 4 0.0632 0.7515 0.024 0.000 0.000 0.976 0.000 0.000
#> GSM152990 3 0.4551 0.5676 0.000 0.344 0.608 0.048 0.000 0.000
#> GSM152991 3 0.6174 0.3841 0.000 0.224 0.416 0.008 0.000 0.352
#> GSM187524 1 0.6751 0.3559 0.524 0.000 0.000 0.136 0.192 0.148
#> GSM187525 1 0.4203 0.5060 0.740 0.000 0.000 0.124 0.000 0.136
#> GSM187526 1 0.1285 0.7428 0.944 0.000 0.000 0.052 0.000 0.004
#> GSM187527 5 0.0146 1.0000 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM152856 5 0.0146 1.0000 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM152857 5 0.0146 1.0000 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM152858 6 0.3945 0.9833 0.380 0.000 0.000 0.000 0.008 0.612
#> GSM152859 6 0.3727 0.9972 0.388 0.000 0.000 0.000 0.000 0.612
#> GSM152860 6 0.3727 0.9972 0.388 0.000 0.000 0.000 0.000 0.612
#> GSM152861 1 0.0000 0.7500 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152862 6 0.3727 0.9972 0.388 0.000 0.000 0.000 0.000 0.612
#> GSM152863 1 0.0865 0.7637 0.964 0.000 0.000 0.000 0.036 0.000
#> GSM152864 1 0.0547 0.7676 0.980 0.000 0.000 0.000 0.020 0.000
#> GSM152865 1 0.0632 0.7691 0.976 0.000 0.000 0.000 0.024 0.000
#> GSM152866 5 0.0146 1.0000 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM152867 1 0.0713 0.7693 0.972 0.000 0.000 0.000 0.028 0.000
#> GSM152868 1 0.0713 0.7693 0.972 0.000 0.000 0.000 0.028 0.000
#> GSM152869 1 0.0260 0.7588 0.992 0.000 0.000 0.000 0.008 0.000
#> GSM152870 6 0.3727 0.9972 0.388 0.000 0.000 0.000 0.000 0.612
#> GSM152871 6 0.3727 0.9972 0.388 0.000 0.000 0.000 0.000 0.612
#> GSM152872 6 0.3727 0.9972 0.388 0.000 0.000 0.000 0.000 0.612
#> GSM152873 5 0.0146 1.0000 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM152874 5 0.0146 1.0000 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM152875 5 0.0146 1.0000 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM152876 5 0.0146 1.0000 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM152877 5 0.0146 1.0000 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM152878 5 0.0146 1.0000 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM152879 5 0.0146 1.0000 0.004 0.000 0.000 0.000 0.996 0.000
#> GSM152880 5 0.0146 1.0000 0.004 0.000 0.000 0.000 0.996 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> MAD:pam 168 2.02e-26 2
#> MAD:pam 152 1.80e-29 3
#> MAD:pam 148 2.44e-30 4
#> MAD:pam 139 2.67e-25 5
#> MAD:pam 128 2.66e-22 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "mclust"]
# you can also extract it by
# res = res_list["MAD:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.949 0.945 0.969 0.3275 0.694 0.694
#> 3 3 0.515 0.831 0.865 0.7119 0.736 0.624
#> 4 4 0.673 0.833 0.901 0.1946 0.890 0.753
#> 5 5 0.625 0.779 0.835 0.1118 0.865 0.613
#> 6 6 0.684 0.606 0.775 0.0576 0.932 0.732
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.964 0.000 1.000
#> GSM152805 2 0.4161 0.908 0.084 0.916
#> GSM152806 2 0.4161 0.908 0.084 0.916
#> GSM152807 2 0.0000 0.964 0.000 1.000
#> GSM152808 2 0.4161 0.908 0.084 0.916
#> GSM152809 2 0.0000 0.964 0.000 1.000
#> GSM152810 2 0.4298 0.905 0.088 0.912
#> GSM152811 2 0.4161 0.908 0.084 0.916
#> GSM152812 2 0.0000 0.964 0.000 1.000
#> GSM152813 2 0.0000 0.964 0.000 1.000
#> GSM152814 2 0.0000 0.964 0.000 1.000
#> GSM152815 2 0.0000 0.964 0.000 1.000
#> GSM152816 2 0.0000 0.964 0.000 1.000
#> GSM152817 2 0.4161 0.908 0.084 0.916
#> GSM152818 2 0.4161 0.908 0.084 0.916
#> GSM152819 2 0.0000 0.964 0.000 1.000
#> GSM152820 2 0.0000 0.964 0.000 1.000
#> GSM152821 2 0.0000 0.964 0.000 1.000
#> GSM153115 2 0.4562 0.914 0.096 0.904
#> GSM153116 2 0.0000 0.964 0.000 1.000
#> GSM153117 2 0.0000 0.964 0.000 1.000
#> GSM153118 2 0.0000 0.964 0.000 1.000
#> GSM153119 2 0.3114 0.931 0.056 0.944
#> GSM153120 2 0.4562 0.914 0.096 0.904
#> GSM153121 2 0.0000 0.964 0.000 1.000
#> GSM153122 2 0.3584 0.922 0.068 0.932
#> GSM153123 2 0.0000 0.964 0.000 1.000
#> GSM153124 2 0.4431 0.916 0.092 0.908
#> GSM153125 2 0.4562 0.914 0.096 0.904
#> GSM153126 2 0.0000 0.964 0.000 1.000
#> GSM153127 2 0.0000 0.964 0.000 1.000
#> GSM153128 2 0.0000 0.964 0.000 1.000
#> GSM153129 2 0.0000 0.964 0.000 1.000
#> GSM153130 2 0.0000 0.964 0.000 1.000
#> GSM153131 2 0.0000 0.964 0.000 1.000
#> GSM153132 2 0.0000 0.964 0.000 1.000
#> GSM153133 2 0.0000 0.964 0.000 1.000
#> GSM153134 2 0.0000 0.964 0.000 1.000
#> GSM153135 2 0.0000 0.964 0.000 1.000
#> GSM153136 2 0.4562 0.914 0.096 0.904
#> GSM153137 2 0.0000 0.964 0.000 1.000
#> GSM153138 2 0.0000 0.964 0.000 1.000
#> GSM153139 2 0.0000 0.964 0.000 1.000
#> GSM153140 2 0.0000 0.964 0.000 1.000
#> GSM153141 2 0.0000 0.964 0.000 1.000
#> GSM153142 2 0.0000 0.964 0.000 1.000
#> GSM153143 2 0.0000 0.964 0.000 1.000
#> GSM153144 2 0.0000 0.964 0.000 1.000
#> GSM153145 2 0.4161 0.908 0.084 0.916
#> GSM153146 2 0.0000 0.964 0.000 1.000
#> GSM153147 2 0.0000 0.964 0.000 1.000
#> GSM153148 2 0.0000 0.964 0.000 1.000
#> GSM153149 2 0.0000 0.964 0.000 1.000
#> GSM153150 2 0.4562 0.914 0.096 0.904
#> GSM153151 2 0.0000 0.964 0.000 1.000
#> GSM153152 2 0.0000 0.964 0.000 1.000
#> GSM153153 2 0.0000 0.964 0.000 1.000
#> GSM153154 2 0.0000 0.964 0.000 1.000
#> GSM153155 2 0.0000 0.964 0.000 1.000
#> GSM153156 2 0.0000 0.964 0.000 1.000
#> GSM153157 2 0.3274 0.928 0.060 0.940
#> GSM153158 2 0.0000 0.964 0.000 1.000
#> GSM153159 2 0.0000 0.964 0.000 1.000
#> GSM153160 2 0.0000 0.964 0.000 1.000
#> GSM153161 2 0.0000 0.964 0.000 1.000
#> GSM153162 2 0.0000 0.964 0.000 1.000
#> GSM153163 2 0.0000 0.964 0.000 1.000
#> GSM153164 2 0.0000 0.964 0.000 1.000
#> GSM153165 2 0.0000 0.964 0.000 1.000
#> GSM153166 2 0.0000 0.964 0.000 1.000
#> GSM153167 2 0.0000 0.964 0.000 1.000
#> GSM153168 2 0.4161 0.908 0.084 0.916
#> GSM153169 2 0.0000 0.964 0.000 1.000
#> GSM153170 2 0.0000 0.964 0.000 1.000
#> GSM153171 2 0.4562 0.914 0.096 0.904
#> GSM153172 2 0.0000 0.964 0.000 1.000
#> GSM153173 2 0.0000 0.964 0.000 1.000
#> GSM153174 2 0.0000 0.964 0.000 1.000
#> GSM153175 2 0.4562 0.914 0.096 0.904
#> GSM153176 2 0.4562 0.914 0.096 0.904
#> GSM153177 2 0.0000 0.964 0.000 1.000
#> GSM152931 2 0.4562 0.914 0.096 0.904
#> GSM152932 2 0.0000 0.964 0.000 1.000
#> GSM152933 2 0.0000 0.964 0.000 1.000
#> GSM152934 2 0.0938 0.959 0.012 0.988
#> GSM152935 2 0.0000 0.964 0.000 1.000
#> GSM152936 2 0.4562 0.914 0.096 0.904
#> GSM152937 2 0.0000 0.964 0.000 1.000
#> GSM152938 2 0.0000 0.964 0.000 1.000
#> GSM152939 2 0.4562 0.914 0.096 0.904
#> GSM152940 2 0.4562 0.914 0.096 0.904
#> GSM152941 1 0.4431 0.891 0.908 0.092
#> GSM152942 2 0.0000 0.964 0.000 1.000
#> GSM152943 2 0.2236 0.948 0.036 0.964
#> GSM152944 2 0.0000 0.964 0.000 1.000
#> GSM152945 2 0.0000 0.964 0.000 1.000
#> GSM152946 2 0.0000 0.964 0.000 1.000
#> GSM152947 2 0.5059 0.902 0.112 0.888
#> GSM152948 2 0.0000 0.964 0.000 1.000
#> GSM152949 2 0.0000 0.964 0.000 1.000
#> GSM152950 2 0.0000 0.964 0.000 1.000
#> GSM152951 2 0.0000 0.964 0.000 1.000
#> GSM152952 2 0.0000 0.964 0.000 1.000
#> GSM152953 2 0.0000 0.964 0.000 1.000
#> GSM152954 2 0.4562 0.914 0.096 0.904
#> GSM152955 2 0.0000 0.964 0.000 1.000
#> GSM152956 2 0.0000 0.964 0.000 1.000
#> GSM152957 2 0.4562 0.914 0.096 0.904
#> GSM152958 2 0.4562 0.914 0.096 0.904
#> GSM152959 2 0.4562 0.914 0.096 0.904
#> GSM152960 2 0.4562 0.914 0.096 0.904
#> GSM152961 2 0.4562 0.914 0.096 0.904
#> GSM152962 2 0.0000 0.964 0.000 1.000
#> GSM152963 2 0.0000 0.964 0.000 1.000
#> GSM152964 2 0.2236 0.944 0.036 0.964
#> GSM152965 2 0.0000 0.964 0.000 1.000
#> GSM152966 2 0.4562 0.914 0.096 0.904
#> GSM152967 2 0.0000 0.964 0.000 1.000
#> GSM152968 2 0.0000 0.964 0.000 1.000
#> GSM152969 2 0.4562 0.914 0.096 0.904
#> GSM152970 2 0.4815 0.908 0.104 0.896
#> GSM152971 2 0.4562 0.914 0.096 0.904
#> GSM152972 2 0.4562 0.914 0.096 0.904
#> GSM152973 2 0.4562 0.914 0.096 0.904
#> GSM152974 2 0.0000 0.964 0.000 1.000
#> GSM152975 2 0.0000 0.964 0.000 1.000
#> GSM152976 2 0.4815 0.908 0.104 0.896
#> GSM152977 2 0.4298 0.911 0.088 0.912
#> GSM152978 2 0.4562 0.914 0.096 0.904
#> GSM152979 2 0.0000 0.964 0.000 1.000
#> GSM152980 2 0.0000 0.964 0.000 1.000
#> GSM152981 2 0.4161 0.908 0.084 0.916
#> GSM152982 2 0.4562 0.914 0.096 0.904
#> GSM152983 2 0.4562 0.914 0.096 0.904
#> GSM152984 2 0.0000 0.964 0.000 1.000
#> GSM152985 1 0.9358 0.410 0.648 0.352
#> GSM152986 2 0.4562 0.914 0.096 0.904
#> GSM152987 1 0.4161 0.898 0.916 0.084
#> GSM152988 2 0.4562 0.914 0.096 0.904
#> GSM152989 2 0.9552 0.456 0.376 0.624
#> GSM152990 2 0.0000 0.964 0.000 1.000
#> GSM152991 2 0.0000 0.964 0.000 1.000
#> GSM187524 1 0.0000 0.978 1.000 0.000
#> GSM187525 1 0.0000 0.978 1.000 0.000
#> GSM187526 1 0.0000 0.978 1.000 0.000
#> GSM187527 1 0.0000 0.978 1.000 0.000
#> GSM152856 1 0.0000 0.978 1.000 0.000
#> GSM152857 1 0.5059 0.864 0.888 0.112
#> GSM152858 1 0.0000 0.978 1.000 0.000
#> GSM152859 1 0.0000 0.978 1.000 0.000
#> GSM152860 1 0.0000 0.978 1.000 0.000
#> GSM152861 1 0.0000 0.978 1.000 0.000
#> GSM152862 1 0.0000 0.978 1.000 0.000
#> GSM152863 1 0.0000 0.978 1.000 0.000
#> GSM152864 1 0.0000 0.978 1.000 0.000
#> GSM152865 1 0.0000 0.978 1.000 0.000
#> GSM152866 1 0.0000 0.978 1.000 0.000
#> GSM152867 1 0.0000 0.978 1.000 0.000
#> GSM152868 1 0.0000 0.978 1.000 0.000
#> GSM152869 1 0.0000 0.978 1.000 0.000
#> GSM152870 1 0.0000 0.978 1.000 0.000
#> GSM152871 1 0.0000 0.978 1.000 0.000
#> GSM152872 1 0.0000 0.978 1.000 0.000
#> GSM152873 1 0.0000 0.978 1.000 0.000
#> GSM152874 1 0.0000 0.978 1.000 0.000
#> GSM152875 1 0.0000 0.978 1.000 0.000
#> GSM152876 1 0.0000 0.978 1.000 0.000
#> GSM152877 1 0.0000 0.978 1.000 0.000
#> GSM152878 1 0.0000 0.978 1.000 0.000
#> GSM152879 1 0.0000 0.978 1.000 0.000
#> GSM152880 1 0.0000 0.978 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 3 0.6307 0.00529 0.000 0.488 0.512
#> GSM152805 3 0.5268 0.69859 0.012 0.212 0.776
#> GSM152806 3 0.5268 0.69859 0.012 0.212 0.776
#> GSM152807 3 0.5905 0.50553 0.000 0.352 0.648
#> GSM152808 3 0.5268 0.69859 0.012 0.212 0.776
#> GSM152809 3 0.5859 0.52536 0.000 0.344 0.656
#> GSM152810 3 0.6034 0.68786 0.036 0.212 0.752
#> GSM152811 3 0.5171 0.70676 0.012 0.204 0.784
#> GSM152812 3 0.4842 0.73925 0.000 0.224 0.776
#> GSM152813 3 0.5254 0.68470 0.000 0.264 0.736
#> GSM152814 3 0.3619 0.81735 0.000 0.136 0.864
#> GSM152815 3 0.4974 0.72404 0.000 0.236 0.764
#> GSM152816 3 0.1860 0.83634 0.000 0.052 0.948
#> GSM152817 3 0.5268 0.69859 0.012 0.212 0.776
#> GSM152818 3 0.5268 0.69859 0.012 0.212 0.776
#> GSM152819 3 0.0000 0.84814 0.000 0.000 1.000
#> GSM152820 3 0.0000 0.84814 0.000 0.000 1.000
#> GSM152821 3 0.3551 0.81744 0.000 0.132 0.868
#> GSM153115 2 0.4741 0.93764 0.020 0.828 0.152
#> GSM153116 3 0.0592 0.84436 0.000 0.012 0.988
#> GSM153117 3 0.0592 0.84963 0.000 0.012 0.988
#> GSM153118 3 0.3412 0.82241 0.000 0.124 0.876
#> GSM153119 3 0.3983 0.77123 0.004 0.144 0.852
#> GSM153120 2 0.5235 0.94055 0.036 0.812 0.152
#> GSM153121 3 0.1031 0.85041 0.000 0.024 0.976
#> GSM153122 3 0.4195 0.77212 0.012 0.136 0.852
#> GSM153123 3 0.2261 0.84367 0.000 0.068 0.932
#> GSM153124 2 0.5506 0.84719 0.016 0.764 0.220
#> GSM153125 2 0.4999 0.94120 0.028 0.820 0.152
#> GSM153126 3 0.1411 0.84651 0.000 0.036 0.964
#> GSM153127 3 0.4504 0.76937 0.000 0.196 0.804
#> GSM153128 3 0.1753 0.83848 0.000 0.048 0.952
#> GSM153129 3 0.0892 0.85021 0.000 0.020 0.980
#> GSM153130 3 0.1289 0.84438 0.000 0.032 0.968
#> GSM153131 3 0.2356 0.83276 0.000 0.072 0.928
#> GSM153132 3 0.0000 0.84814 0.000 0.000 1.000
#> GSM153133 3 0.2959 0.83246 0.000 0.100 0.900
#> GSM153134 3 0.0237 0.84901 0.000 0.004 0.996
#> GSM153135 3 0.5363 0.66479 0.000 0.276 0.724
#> GSM153136 2 0.5119 0.94204 0.032 0.816 0.152
#> GSM153137 3 0.6204 0.28681 0.000 0.424 0.576
#> GSM153138 3 0.3551 0.81744 0.000 0.132 0.868
#> GSM153139 3 0.0747 0.84641 0.000 0.016 0.984
#> GSM153140 3 0.5291 0.67256 0.000 0.268 0.732
#> GSM153141 3 0.5216 0.69035 0.000 0.260 0.740
#> GSM153142 3 0.1163 0.84463 0.000 0.028 0.972
#> GSM153143 3 0.5058 0.71308 0.000 0.244 0.756
#> GSM153144 3 0.3340 0.82347 0.000 0.120 0.880
#> GSM153145 3 0.5268 0.69859 0.012 0.212 0.776
#> GSM153146 3 0.3551 0.81744 0.000 0.132 0.868
#> GSM153147 3 0.1411 0.85079 0.000 0.036 0.964
#> GSM153148 3 0.4178 0.79150 0.000 0.172 0.828
#> GSM153149 3 0.2066 0.84624 0.000 0.060 0.940
#> GSM153150 2 0.5119 0.94204 0.032 0.816 0.152
#> GSM153151 3 0.2356 0.84381 0.000 0.072 0.928
#> GSM153152 3 0.0592 0.84990 0.000 0.012 0.988
#> GSM153153 3 0.2878 0.83516 0.000 0.096 0.904
#> GSM153154 3 0.0237 0.84713 0.000 0.004 0.996
#> GSM153155 3 0.3551 0.81573 0.000 0.132 0.868
#> GSM153156 3 0.0592 0.84856 0.000 0.012 0.988
#> GSM153157 3 0.3918 0.77448 0.004 0.140 0.856
#> GSM153158 3 0.0237 0.84713 0.000 0.004 0.996
#> GSM153159 3 0.1031 0.84505 0.000 0.024 0.976
#> GSM153160 3 0.1529 0.84536 0.000 0.040 0.960
#> GSM153161 3 0.4842 0.73865 0.000 0.224 0.776
#> GSM153162 3 0.0747 0.84942 0.000 0.016 0.984
#> GSM153163 3 0.1031 0.84498 0.000 0.024 0.976
#> GSM153164 3 0.0592 0.84945 0.000 0.012 0.988
#> GSM153165 3 0.0892 0.84669 0.000 0.020 0.980
#> GSM153166 3 0.0747 0.84965 0.000 0.016 0.984
#> GSM153167 3 0.2448 0.84155 0.000 0.076 0.924
#> GSM153168 3 0.5268 0.69859 0.012 0.212 0.776
#> GSM153169 3 0.1289 0.84372 0.000 0.032 0.968
#> GSM153170 3 0.0237 0.84868 0.000 0.004 0.996
#> GSM153171 2 0.5119 0.94204 0.032 0.816 0.152
#> GSM153172 3 0.3551 0.81744 0.000 0.132 0.868
#> GSM153173 3 0.1031 0.84532 0.000 0.024 0.976
#> GSM153174 3 0.3686 0.81856 0.000 0.140 0.860
#> GSM153175 2 0.4172 0.92715 0.004 0.840 0.156
#> GSM153176 2 0.4233 0.92058 0.004 0.836 0.160
#> GSM153177 3 0.0747 0.84965 0.000 0.016 0.984
#> GSM152931 2 0.4934 0.93863 0.024 0.820 0.156
#> GSM152932 3 0.3340 0.82298 0.000 0.120 0.880
#> GSM152933 3 0.1753 0.84862 0.000 0.048 0.952
#> GSM152934 3 0.6859 0.46713 0.024 0.356 0.620
#> GSM152935 3 0.1860 0.84854 0.000 0.052 0.948
#> GSM152936 2 0.5119 0.94204 0.032 0.816 0.152
#> GSM152937 3 0.2878 0.83349 0.000 0.096 0.904
#> GSM152938 3 0.2537 0.83916 0.000 0.080 0.920
#> GSM152939 2 0.3941 0.92426 0.000 0.844 0.156
#> GSM152940 2 0.5235 0.94055 0.036 0.812 0.152
#> GSM152941 2 0.6744 0.51522 0.300 0.668 0.032
#> GSM152942 3 0.2448 0.83943 0.000 0.076 0.924
#> GSM152943 3 0.6621 0.62860 0.032 0.284 0.684
#> GSM152944 3 0.1031 0.84532 0.000 0.024 0.976
#> GSM152945 3 0.3784 0.81911 0.004 0.132 0.864
#> GSM152946 3 0.6252 0.20874 0.000 0.444 0.556
#> GSM152947 2 0.5346 0.93919 0.040 0.808 0.152
#> GSM152948 3 0.6126 0.36871 0.000 0.400 0.600
#> GSM152949 3 0.0892 0.85060 0.000 0.020 0.980
#> GSM152950 3 0.0892 0.85021 0.000 0.020 0.980
#> GSM152951 3 0.5397 0.65803 0.000 0.280 0.720
#> GSM152952 3 0.5138 0.70239 0.000 0.252 0.748
#> GSM152953 3 0.4291 0.78144 0.000 0.180 0.820
#> GSM152954 2 0.5119 0.94204 0.032 0.816 0.152
#> GSM152955 3 0.4172 0.81784 0.004 0.156 0.840
#> GSM152956 3 0.4452 0.77362 0.000 0.192 0.808
#> GSM152957 2 0.4602 0.93544 0.016 0.832 0.152
#> GSM152958 2 0.5119 0.94204 0.032 0.816 0.152
#> GSM152959 2 0.5119 0.94204 0.032 0.816 0.152
#> GSM152960 2 0.5180 0.94008 0.032 0.812 0.156
#> GSM152961 2 0.5435 0.93222 0.048 0.808 0.144
#> GSM152962 3 0.0747 0.85016 0.000 0.016 0.984
#> GSM152963 3 0.4399 0.77726 0.000 0.188 0.812
#> GSM152964 3 0.3213 0.82080 0.008 0.092 0.900
#> GSM152965 3 0.3482 0.82008 0.000 0.128 0.872
#> GSM152966 2 0.4999 0.94120 0.028 0.820 0.152
#> GSM152967 3 0.4291 0.78571 0.000 0.180 0.820
#> GSM152968 3 0.0237 0.84868 0.000 0.004 0.996
#> GSM152969 2 0.5119 0.94204 0.032 0.816 0.152
#> GSM152970 2 0.5558 0.93433 0.048 0.800 0.152
#> GSM152971 2 0.4999 0.94120 0.028 0.820 0.152
#> GSM152972 2 0.5119 0.94204 0.032 0.816 0.152
#> GSM152973 2 0.4235 0.90918 0.000 0.824 0.176
#> GSM152974 3 0.3482 0.82003 0.000 0.128 0.872
#> GSM152975 3 0.6172 0.60619 0.012 0.308 0.680
#> GSM152976 2 0.5235 0.94088 0.036 0.812 0.152
#> GSM152977 2 0.5541 0.79489 0.008 0.740 0.252
#> GSM152978 2 0.5235 0.94055 0.036 0.812 0.152
#> GSM152979 3 0.0892 0.84669 0.000 0.020 0.980
#> GSM152980 3 0.4002 0.80625 0.000 0.160 0.840
#> GSM152981 3 0.5268 0.69859 0.012 0.212 0.776
#> GSM152982 2 0.4514 0.93143 0.012 0.832 0.156
#> GSM152983 2 0.5119 0.94204 0.032 0.816 0.152
#> GSM152984 2 0.5988 0.54942 0.000 0.632 0.368
#> GSM152985 2 0.5812 0.58440 0.264 0.724 0.012
#> GSM152986 2 0.5119 0.94204 0.032 0.816 0.152
#> GSM152987 2 0.5810 0.41785 0.336 0.664 0.000
#> GSM152988 2 0.3941 0.92426 0.000 0.844 0.156
#> GSM152989 2 0.6168 0.88168 0.096 0.780 0.124
#> GSM152990 3 0.0892 0.84669 0.000 0.020 0.980
#> GSM152991 3 0.0000 0.84814 0.000 0.000 1.000
#> GSM187524 1 0.0237 0.99024 0.996 0.004 0.000
#> GSM187525 1 0.0237 0.99024 0.996 0.004 0.000
#> GSM187526 1 0.0237 0.99024 0.996 0.004 0.000
#> GSM187527 1 0.0237 0.98980 0.996 0.004 0.000
#> GSM152856 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152857 1 0.4409 0.78678 0.824 0.172 0.004
#> GSM152858 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152859 1 0.0237 0.99024 0.996 0.004 0.000
#> GSM152860 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152861 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152862 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152863 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152864 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152866 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152867 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152870 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152871 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152873 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152874 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152875 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152876 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152877 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152878 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152879 1 0.0000 0.99287 1.000 0.000 0.000
#> GSM152880 1 0.0000 0.99287 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.3982 0.7926 0.000 0.776 0.004 0.220
#> GSM152805 3 0.5345 0.1255 0.000 0.428 0.560 0.012
#> GSM152806 3 0.0657 0.8557 0.000 0.004 0.984 0.012
#> GSM152807 2 0.2647 0.8614 0.000 0.880 0.000 0.120
#> GSM152808 3 0.0657 0.8557 0.000 0.004 0.984 0.012
#> GSM152809 2 0.2647 0.8614 0.000 0.880 0.000 0.120
#> GSM152810 3 0.2958 0.8190 0.004 0.028 0.896 0.072
#> GSM152811 3 0.0937 0.8581 0.000 0.012 0.976 0.012
#> GSM152812 2 0.2760 0.8593 0.000 0.872 0.000 0.128
#> GSM152813 2 0.2589 0.8619 0.000 0.884 0.000 0.116
#> GSM152814 2 0.2647 0.8614 0.000 0.880 0.000 0.120
#> GSM152815 2 0.2760 0.8593 0.000 0.872 0.000 0.128
#> GSM152816 2 0.4244 0.7364 0.000 0.800 0.168 0.032
#> GSM152817 3 0.0657 0.8557 0.000 0.004 0.984 0.012
#> GSM152818 3 0.1488 0.8532 0.000 0.032 0.956 0.012
#> GSM152819 2 0.2742 0.8230 0.000 0.900 0.076 0.024
#> GSM152820 2 0.2111 0.8443 0.000 0.932 0.044 0.024
#> GSM152821 2 0.2589 0.8639 0.000 0.884 0.000 0.116
#> GSM153115 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM153116 2 0.4204 0.6717 0.000 0.788 0.192 0.020
#> GSM153117 2 0.0707 0.8555 0.000 0.980 0.000 0.020
#> GSM153118 2 0.2345 0.8667 0.000 0.900 0.000 0.100
#> GSM153119 3 0.2021 0.8553 0.000 0.040 0.936 0.024
#> GSM153120 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM153121 2 0.3581 0.7713 0.000 0.852 0.116 0.032
#> GSM153122 3 0.2036 0.8559 0.000 0.032 0.936 0.032
#> GSM153123 2 0.2081 0.8683 0.000 0.916 0.000 0.084
#> GSM153124 4 0.3751 0.6762 0.000 0.196 0.004 0.800
#> GSM153125 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM153126 2 0.4057 0.7375 0.000 0.816 0.152 0.032
#> GSM153127 2 0.2760 0.8593 0.000 0.872 0.000 0.128
#> GSM153128 3 0.6162 0.6073 0.000 0.304 0.620 0.076
#> GSM153129 2 0.0707 0.8556 0.000 0.980 0.000 0.020
#> GSM153130 2 0.3907 0.7480 0.000 0.828 0.140 0.032
#> GSM153131 2 0.3652 0.8055 0.000 0.856 0.092 0.052
#> GSM153132 2 0.0592 0.8542 0.000 0.984 0.000 0.016
#> GSM153133 2 0.2216 0.8684 0.000 0.908 0.000 0.092
#> GSM153134 2 0.0707 0.8529 0.000 0.980 0.000 0.020
#> GSM153135 2 0.2760 0.8593 0.000 0.872 0.000 0.128
#> GSM153136 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM153137 2 0.3266 0.8348 0.000 0.832 0.000 0.168
#> GSM153138 2 0.3249 0.8526 0.000 0.852 0.008 0.140
#> GSM153139 2 0.3279 0.7894 0.000 0.872 0.096 0.032
#> GSM153140 2 0.2589 0.8619 0.000 0.884 0.000 0.116
#> GSM153141 2 0.2760 0.8593 0.000 0.872 0.000 0.128
#> GSM153142 3 0.5432 0.6017 0.000 0.316 0.652 0.032
#> GSM153143 2 0.2704 0.8621 0.000 0.876 0.000 0.124
#> GSM153144 2 0.2704 0.8634 0.000 0.876 0.000 0.124
#> GSM153145 3 0.0657 0.8557 0.000 0.004 0.984 0.012
#> GSM153146 2 0.2408 0.8657 0.000 0.896 0.000 0.104
#> GSM153147 2 0.1022 0.8582 0.000 0.968 0.000 0.032
#> GSM153148 2 0.2760 0.8593 0.000 0.872 0.000 0.128
#> GSM153149 2 0.1940 0.8682 0.000 0.924 0.000 0.076
#> GSM153150 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM153151 2 0.1635 0.8634 0.000 0.948 0.008 0.044
#> GSM153152 2 0.0469 0.8527 0.000 0.988 0.000 0.012
#> GSM153153 2 0.2408 0.8661 0.000 0.896 0.000 0.104
#> GSM153154 2 0.0707 0.8490 0.000 0.980 0.000 0.020
#> GSM153155 2 0.2647 0.8623 0.000 0.880 0.000 0.120
#> GSM153156 2 0.3638 0.7675 0.000 0.848 0.120 0.032
#> GSM153157 3 0.1936 0.8565 0.000 0.032 0.940 0.028
#> GSM153158 2 0.0592 0.8542 0.000 0.984 0.000 0.016
#> GSM153159 2 0.4289 0.7149 0.000 0.796 0.172 0.032
#> GSM153160 2 0.4057 0.7375 0.000 0.816 0.152 0.032
#> GSM153161 2 0.2647 0.8614 0.000 0.880 0.000 0.120
#> GSM153162 2 0.1022 0.8485 0.000 0.968 0.000 0.032
#> GSM153163 2 0.3907 0.7494 0.000 0.828 0.140 0.032
#> GSM153164 2 0.0921 0.8609 0.000 0.972 0.000 0.028
#> GSM153165 2 0.3523 0.7752 0.000 0.856 0.112 0.032
#> GSM153166 2 0.0817 0.8565 0.000 0.976 0.000 0.024
#> GSM153167 2 0.1302 0.8624 0.000 0.956 0.000 0.044
#> GSM153168 3 0.0657 0.8557 0.000 0.004 0.984 0.012
#> GSM153169 2 0.4152 0.7269 0.000 0.808 0.160 0.032
#> GSM153170 2 0.1022 0.8485 0.000 0.968 0.000 0.032
#> GSM153171 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM153172 2 0.2589 0.8619 0.000 0.884 0.000 0.116
#> GSM153173 2 0.3803 0.7554 0.000 0.836 0.132 0.032
#> GSM153174 2 0.2345 0.8679 0.000 0.900 0.000 0.100
#> GSM153175 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM153176 4 0.4259 0.7581 0.000 0.128 0.056 0.816
#> GSM153177 2 0.0707 0.8569 0.000 0.980 0.000 0.020
#> GSM152931 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152932 2 0.2647 0.8644 0.000 0.880 0.000 0.120
#> GSM152933 2 0.1867 0.8680 0.000 0.928 0.000 0.072
#> GSM152934 4 0.7503 0.1175 0.000 0.212 0.300 0.488
#> GSM152935 2 0.1557 0.8652 0.000 0.944 0.000 0.056
#> GSM152936 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152937 3 0.5740 0.7071 0.000 0.208 0.700 0.092
#> GSM152938 2 0.4127 0.7626 0.000 0.824 0.124 0.052
#> GSM152939 4 0.2032 0.8924 0.000 0.028 0.036 0.936
#> GSM152940 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152941 4 0.3486 0.7069 0.188 0.000 0.000 0.812
#> GSM152942 2 0.4713 0.6936 0.000 0.776 0.172 0.052
#> GSM152943 2 0.7893 -0.0592 0.000 0.376 0.324 0.300
#> GSM152944 2 0.3149 0.7962 0.000 0.880 0.088 0.032
#> GSM152945 2 0.7386 0.2144 0.000 0.496 0.320 0.184
#> GSM152946 2 0.3448 0.8390 0.000 0.828 0.004 0.168
#> GSM152947 4 0.1151 0.9125 0.008 0.024 0.000 0.968
#> GSM152948 2 0.2589 0.8619 0.000 0.884 0.000 0.116
#> GSM152949 2 0.1022 0.8485 0.000 0.968 0.000 0.032
#> GSM152950 2 0.0592 0.8528 0.000 0.984 0.000 0.016
#> GSM152951 2 0.2589 0.8619 0.000 0.884 0.000 0.116
#> GSM152952 2 0.2760 0.8593 0.000 0.872 0.000 0.128
#> GSM152953 2 0.2647 0.8614 0.000 0.880 0.000 0.120
#> GSM152954 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152955 2 0.7446 -0.1678 0.000 0.432 0.396 0.172
#> GSM152956 2 0.2760 0.8593 0.000 0.872 0.000 0.128
#> GSM152957 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152958 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152959 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152960 4 0.1004 0.9163 0.000 0.024 0.004 0.972
#> GSM152961 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152962 2 0.0707 0.8555 0.000 0.980 0.000 0.020
#> GSM152963 2 0.2760 0.8593 0.000 0.872 0.000 0.128
#> GSM152964 3 0.5332 0.7382 0.000 0.124 0.748 0.128
#> GSM152965 2 0.2589 0.8648 0.000 0.884 0.000 0.116
#> GSM152966 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152967 2 0.2704 0.8621 0.000 0.876 0.000 0.124
#> GSM152968 2 0.0707 0.8490 0.000 0.980 0.000 0.020
#> GSM152969 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152970 4 0.1004 0.9159 0.004 0.024 0.000 0.972
#> GSM152971 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152972 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152973 4 0.3286 0.8368 0.000 0.080 0.044 0.876
#> GSM152974 2 0.2704 0.8621 0.000 0.876 0.000 0.124
#> GSM152975 2 0.3942 0.7759 0.000 0.764 0.000 0.236
#> GSM152976 4 0.1284 0.9118 0.000 0.024 0.012 0.964
#> GSM152977 4 0.5066 0.7088 0.000 0.088 0.148 0.764
#> GSM152978 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152979 2 0.3694 0.7636 0.000 0.844 0.124 0.032
#> GSM152980 2 0.3937 0.8049 0.000 0.800 0.012 0.188
#> GSM152981 3 0.0657 0.8557 0.000 0.004 0.984 0.012
#> GSM152982 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152983 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152984 4 0.5693 0.0803 0.000 0.472 0.024 0.504
#> GSM152985 4 0.3400 0.7150 0.180 0.000 0.000 0.820
#> GSM152986 4 0.0817 0.9185 0.000 0.024 0.000 0.976
#> GSM152987 4 0.3610 0.6939 0.200 0.000 0.000 0.800
#> GSM152988 4 0.2131 0.8900 0.000 0.032 0.036 0.932
#> GSM152989 4 0.2861 0.8162 0.096 0.016 0.000 0.888
#> GSM152990 2 0.3149 0.7966 0.000 0.880 0.088 0.032
#> GSM152991 2 0.5452 0.2570 0.000 0.616 0.360 0.024
#> GSM187524 1 0.0657 0.9848 0.984 0.000 0.012 0.004
#> GSM187525 1 0.0657 0.9848 0.984 0.000 0.012 0.004
#> GSM187526 1 0.0657 0.9848 0.984 0.000 0.012 0.004
#> GSM187527 1 0.1211 0.9452 0.960 0.000 0.000 0.040
#> GSM152856 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152857 1 0.3067 0.8477 0.880 0.008 0.008 0.104
#> GSM152858 1 0.0376 0.9866 0.992 0.000 0.004 0.004
#> GSM152859 1 0.0657 0.9848 0.984 0.000 0.012 0.004
#> GSM152860 1 0.0657 0.9848 0.984 0.000 0.012 0.004
#> GSM152861 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152862 1 0.0657 0.9848 0.984 0.000 0.012 0.004
#> GSM152863 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152864 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152866 1 0.0657 0.9848 0.984 0.000 0.012 0.004
#> GSM152867 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152868 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152870 1 0.0657 0.9848 0.984 0.000 0.012 0.004
#> GSM152871 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152872 1 0.0657 0.9848 0.984 0.000 0.012 0.004
#> GSM152873 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152875 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152876 1 0.0469 0.9779 0.988 0.000 0.000 0.012
#> GSM152877 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152878 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152879 1 0.0000 0.9881 1.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.9881 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.2661 0.79286 0.000 0.888 0.056 0.056 0.000
#> GSM152805 5 0.4718 0.73291 0.000 0.092 0.180 0.000 0.728
#> GSM152806 5 0.1410 0.89206 0.000 0.000 0.060 0.000 0.940
#> GSM152807 2 0.1471 0.80060 0.000 0.952 0.004 0.024 0.020
#> GSM152808 5 0.1410 0.89206 0.000 0.000 0.060 0.000 0.940
#> GSM152809 2 0.1399 0.79878 0.000 0.952 0.000 0.028 0.020
#> GSM152810 5 0.5098 0.81033 0.032 0.008 0.180 0.044 0.736
#> GSM152811 5 0.1892 0.89372 0.000 0.000 0.080 0.004 0.916
#> GSM152812 2 0.1310 0.79915 0.000 0.956 0.000 0.024 0.020
#> GSM152813 2 0.1403 0.80907 0.000 0.952 0.024 0.024 0.000
#> GSM152814 2 0.0865 0.80744 0.000 0.972 0.024 0.004 0.000
#> GSM152815 2 0.1310 0.79915 0.000 0.956 0.000 0.024 0.020
#> GSM152816 3 0.2909 0.79843 0.000 0.140 0.848 0.000 0.012
#> GSM152817 5 0.1410 0.89206 0.000 0.000 0.060 0.000 0.940
#> GSM152818 5 0.2450 0.88233 0.000 0.028 0.076 0.000 0.896
#> GSM152819 3 0.4283 0.45140 0.000 0.456 0.544 0.000 0.000
#> GSM152820 3 0.4114 0.63793 0.000 0.376 0.624 0.000 0.000
#> GSM152821 2 0.1357 0.80519 0.000 0.948 0.048 0.004 0.000
#> GSM153115 4 0.2017 0.91154 0.000 0.080 0.008 0.912 0.000
#> GSM153116 3 0.4060 0.65685 0.000 0.360 0.640 0.000 0.000
#> GSM153117 2 0.4268 -0.00824 0.000 0.556 0.444 0.000 0.000
#> GSM153118 2 0.1792 0.79362 0.000 0.916 0.084 0.000 0.000
#> GSM153119 5 0.3109 0.82745 0.000 0.000 0.200 0.000 0.800
#> GSM153120 4 0.2233 0.91153 0.000 0.080 0.016 0.904 0.000
#> GSM153121 3 0.2605 0.80569 0.000 0.148 0.852 0.000 0.000
#> GSM153122 5 0.2929 0.84459 0.000 0.000 0.180 0.000 0.820
#> GSM153123 2 0.3395 0.64447 0.000 0.764 0.236 0.000 0.000
#> GSM153124 4 0.3890 0.74432 0.000 0.252 0.012 0.736 0.000
#> GSM153125 4 0.2411 0.90169 0.000 0.108 0.008 0.884 0.000
#> GSM153126 3 0.2969 0.78814 0.000 0.128 0.852 0.000 0.020
#> GSM153127 2 0.1310 0.79915 0.000 0.956 0.000 0.024 0.020
#> GSM153128 3 0.4703 0.61581 0.000 0.096 0.752 0.008 0.144
#> GSM153129 2 0.4074 0.33910 0.000 0.636 0.364 0.000 0.000
#> GSM153130 3 0.3106 0.78789 0.000 0.132 0.844 0.000 0.024
#> GSM153131 3 0.3366 0.78812 0.000 0.232 0.768 0.000 0.000
#> GSM153132 3 0.4242 0.51315 0.000 0.428 0.572 0.000 0.000
#> GSM153133 2 0.3177 0.68598 0.000 0.792 0.208 0.000 0.000
#> GSM153134 2 0.4015 0.39796 0.000 0.652 0.348 0.000 0.000
#> GSM153135 2 0.1310 0.79915 0.000 0.956 0.000 0.024 0.020
#> GSM153136 4 0.2130 0.91170 0.000 0.080 0.012 0.908 0.000
#> GSM153137 2 0.2297 0.77506 0.000 0.912 0.008 0.060 0.020
#> GSM153138 2 0.2072 0.79250 0.000 0.928 0.036 0.020 0.016
#> GSM153139 3 0.2732 0.80544 0.000 0.160 0.840 0.000 0.000
#> GSM153140 2 0.0693 0.80690 0.000 0.980 0.008 0.012 0.000
#> GSM153141 2 0.1310 0.79915 0.000 0.956 0.000 0.024 0.020
#> GSM153142 3 0.3602 0.55388 0.000 0.024 0.796 0.000 0.180
#> GSM153143 2 0.1560 0.80804 0.000 0.948 0.020 0.028 0.004
#> GSM153144 2 0.2891 0.72316 0.000 0.824 0.176 0.000 0.000
#> GSM153145 5 0.1410 0.89206 0.000 0.000 0.060 0.000 0.940
#> GSM153146 2 0.1704 0.80019 0.000 0.928 0.068 0.004 0.000
#> GSM153147 3 0.4300 0.36207 0.000 0.476 0.524 0.000 0.000
#> GSM153148 2 0.1310 0.79915 0.000 0.956 0.000 0.024 0.020
#> GSM153149 2 0.2773 0.73324 0.000 0.836 0.164 0.000 0.000
#> GSM153150 4 0.2233 0.91183 0.000 0.080 0.016 0.904 0.000
#> GSM153151 2 0.3861 0.55635 0.000 0.712 0.284 0.000 0.004
#> GSM153152 2 0.3983 0.41708 0.000 0.660 0.340 0.000 0.000
#> GSM153153 2 0.1544 0.80004 0.000 0.932 0.068 0.000 0.000
#> GSM153154 3 0.3913 0.70699 0.000 0.324 0.676 0.000 0.000
#> GSM153155 2 0.1282 0.80526 0.000 0.952 0.044 0.004 0.000
#> GSM153156 3 0.2629 0.79992 0.000 0.136 0.860 0.000 0.004
#> GSM153157 5 0.2929 0.84652 0.000 0.000 0.180 0.000 0.820
#> GSM153158 3 0.3966 0.69320 0.000 0.336 0.664 0.000 0.000
#> GSM153159 3 0.3593 0.70136 0.000 0.084 0.828 0.000 0.088
#> GSM153160 3 0.3016 0.79088 0.000 0.132 0.848 0.000 0.020
#> GSM153161 2 0.1310 0.79915 0.000 0.956 0.000 0.024 0.020
#> GSM153162 3 0.3661 0.75524 0.000 0.276 0.724 0.000 0.000
#> GSM153163 3 0.2818 0.79457 0.000 0.132 0.856 0.000 0.012
#> GSM153164 2 0.3508 0.61872 0.000 0.748 0.252 0.000 0.000
#> GSM153165 3 0.2605 0.80598 0.000 0.148 0.852 0.000 0.000
#> GSM153166 2 0.3837 0.50315 0.000 0.692 0.308 0.000 0.000
#> GSM153167 2 0.3857 0.50201 0.000 0.688 0.312 0.000 0.000
#> GSM153168 5 0.1410 0.89206 0.000 0.000 0.060 0.000 0.940
#> GSM153169 3 0.3060 0.78614 0.000 0.128 0.848 0.000 0.024
#> GSM153170 3 0.3395 0.78011 0.000 0.236 0.764 0.000 0.000
#> GSM153171 4 0.2017 0.91154 0.000 0.080 0.008 0.912 0.000
#> GSM153172 2 0.1792 0.79323 0.000 0.916 0.084 0.000 0.000
#> GSM153173 3 0.2818 0.79457 0.000 0.132 0.856 0.000 0.012
#> GSM153174 2 0.3707 0.56524 0.000 0.716 0.284 0.000 0.000
#> GSM153175 4 0.2249 0.90821 0.000 0.096 0.008 0.896 0.000
#> GSM153176 4 0.4066 0.77585 0.000 0.044 0.188 0.768 0.000
#> GSM153177 2 0.3684 0.56509 0.000 0.720 0.280 0.000 0.000
#> GSM152931 4 0.2513 0.89621 0.000 0.116 0.008 0.876 0.000
#> GSM152932 2 0.2561 0.75142 0.000 0.856 0.144 0.000 0.000
#> GSM152933 2 0.3143 0.69101 0.000 0.796 0.204 0.000 0.000
#> GSM152934 4 0.4921 0.77040 0.000 0.184 0.084 0.724 0.008
#> GSM152935 2 0.3932 0.42987 0.000 0.672 0.328 0.000 0.000
#> GSM152936 4 0.2130 0.91184 0.000 0.080 0.012 0.908 0.000
#> GSM152937 3 0.4810 0.56219 0.000 0.092 0.740 0.008 0.160
#> GSM152938 3 0.3143 0.79670 0.000 0.204 0.796 0.000 0.000
#> GSM152939 4 0.3921 0.83904 0.000 0.128 0.072 0.800 0.000
#> GSM152940 4 0.2130 0.91184 0.000 0.080 0.012 0.908 0.000
#> GSM152941 4 0.5973 0.40616 0.316 0.012 0.084 0.584 0.004
#> GSM152942 3 0.2674 0.80084 0.000 0.140 0.856 0.000 0.004
#> GSM152943 2 0.5390 0.37155 0.000 0.608 0.048 0.332 0.012
#> GSM152944 3 0.2773 0.80518 0.000 0.164 0.836 0.000 0.000
#> GSM152945 2 0.4452 0.72404 0.000 0.772 0.164 0.032 0.032
#> GSM152946 2 0.3019 0.79187 0.000 0.864 0.088 0.048 0.000
#> GSM152947 4 0.2511 0.90551 0.000 0.080 0.028 0.892 0.000
#> GSM152948 2 0.1399 0.79878 0.000 0.952 0.000 0.028 0.020
#> GSM152949 3 0.3612 0.76217 0.000 0.268 0.732 0.000 0.000
#> GSM152950 3 0.4114 0.63573 0.000 0.376 0.624 0.000 0.000
#> GSM152951 2 0.1153 0.80338 0.000 0.964 0.004 0.024 0.008
#> GSM152952 2 0.1310 0.79915 0.000 0.956 0.000 0.024 0.020
#> GSM152953 2 0.1646 0.80032 0.000 0.944 0.004 0.032 0.020
#> GSM152954 4 0.2130 0.91208 0.000 0.080 0.012 0.908 0.000
#> GSM152955 3 0.5770 0.42339 0.000 0.392 0.540 0.040 0.028
#> GSM152956 2 0.1310 0.79915 0.000 0.956 0.000 0.024 0.020
#> GSM152957 4 0.2595 0.90570 0.000 0.080 0.032 0.888 0.000
#> GSM152958 4 0.1892 0.91181 0.000 0.080 0.004 0.916 0.000
#> GSM152959 4 0.2830 0.90093 0.000 0.080 0.044 0.876 0.000
#> GSM152960 4 0.2511 0.90894 0.000 0.080 0.028 0.892 0.000
#> GSM152961 4 0.1892 0.91181 0.000 0.080 0.004 0.916 0.000
#> GSM152962 3 0.4192 0.58650 0.000 0.404 0.596 0.000 0.000
#> GSM152963 2 0.1310 0.79915 0.000 0.956 0.000 0.024 0.020
#> GSM152964 5 0.6462 0.62310 0.012 0.080 0.264 0.040 0.604
#> GSM152965 2 0.1831 0.79946 0.000 0.920 0.076 0.004 0.000
#> GSM152966 4 0.2249 0.90813 0.000 0.096 0.008 0.896 0.000
#> GSM152967 2 0.1741 0.80897 0.000 0.936 0.040 0.024 0.000
#> GSM152968 3 0.4045 0.66645 0.000 0.356 0.644 0.000 0.000
#> GSM152969 4 0.2130 0.91170 0.000 0.080 0.012 0.908 0.000
#> GSM152970 4 0.2595 0.90427 0.000 0.080 0.032 0.888 0.000
#> GSM152971 4 0.2305 0.90933 0.000 0.092 0.012 0.896 0.000
#> GSM152972 4 0.2017 0.91194 0.000 0.080 0.008 0.912 0.000
#> GSM152973 4 0.4681 0.72779 0.000 0.084 0.188 0.728 0.000
#> GSM152974 2 0.2516 0.75320 0.000 0.860 0.140 0.000 0.000
#> GSM152975 2 0.4059 0.72244 0.000 0.776 0.172 0.052 0.000
#> GSM152976 4 0.2830 0.90440 0.000 0.080 0.044 0.876 0.000
#> GSM152977 4 0.4127 0.82070 0.000 0.080 0.136 0.784 0.000
#> GSM152978 4 0.2233 0.91153 0.000 0.080 0.016 0.904 0.000
#> GSM152979 3 0.2605 0.80569 0.000 0.148 0.852 0.000 0.000
#> GSM152980 2 0.2853 0.74087 0.000 0.876 0.052 0.072 0.000
#> GSM152981 5 0.1478 0.89318 0.000 0.000 0.064 0.000 0.936
#> GSM152982 4 0.2932 0.89805 0.000 0.104 0.032 0.864 0.000
#> GSM152983 4 0.2130 0.91184 0.000 0.080 0.012 0.908 0.000
#> GSM152984 3 0.6273 -0.01956 0.000 0.148 0.436 0.416 0.000
#> GSM152985 4 0.5028 0.61898 0.220 0.012 0.064 0.704 0.000
#> GSM152986 4 0.2017 0.91154 0.000 0.080 0.008 0.912 0.000
#> GSM152987 4 0.5474 0.31425 0.348 0.000 0.076 0.576 0.000
#> GSM152988 4 0.4364 0.79042 0.000 0.112 0.120 0.768 0.000
#> GSM152989 4 0.3753 0.85996 0.048 0.056 0.052 0.844 0.000
#> GSM152990 3 0.2929 0.80049 0.000 0.180 0.820 0.000 0.000
#> GSM152991 3 0.4880 0.64371 0.000 0.348 0.616 0.000 0.036
#> GSM187524 1 0.3236 0.90802 0.872 0.000 0.052 0.044 0.032
#> GSM187525 1 0.3236 0.90802 0.872 0.000 0.052 0.044 0.032
#> GSM187526 1 0.3236 0.90802 0.872 0.000 0.052 0.044 0.032
#> GSM187527 1 0.0912 0.93695 0.972 0.000 0.012 0.016 0.000
#> GSM152856 1 0.1251 0.93899 0.956 0.000 0.000 0.036 0.008
#> GSM152857 1 0.4365 0.74671 0.784 0.012 0.052 0.148 0.004
#> GSM152858 1 0.1750 0.93070 0.936 0.000 0.036 0.028 0.000
#> GSM152859 1 0.3236 0.90802 0.872 0.000 0.052 0.044 0.032
#> GSM152860 1 0.3165 0.90987 0.876 0.000 0.048 0.044 0.032
#> GSM152861 1 0.0162 0.94128 0.996 0.000 0.000 0.004 0.000
#> GSM152862 1 0.3165 0.90987 0.876 0.000 0.048 0.044 0.032
#> GSM152863 1 0.0579 0.94036 0.984 0.000 0.008 0.008 0.000
#> GSM152864 1 0.1251 0.93899 0.956 0.000 0.000 0.036 0.008
#> GSM152865 1 0.0451 0.94147 0.988 0.000 0.000 0.008 0.004
#> GSM152866 1 0.1907 0.92877 0.928 0.000 0.028 0.044 0.000
#> GSM152867 1 0.1251 0.93899 0.956 0.000 0.000 0.036 0.008
#> GSM152868 1 0.1251 0.93899 0.956 0.000 0.000 0.036 0.008
#> GSM152869 1 0.1251 0.93899 0.956 0.000 0.000 0.036 0.008
#> GSM152870 1 0.3236 0.90802 0.872 0.000 0.052 0.044 0.032
#> GSM152871 1 0.0162 0.94176 0.996 0.000 0.004 0.000 0.000
#> GSM152872 1 0.1997 0.92716 0.924 0.000 0.040 0.036 0.000
#> GSM152873 1 0.1251 0.93899 0.956 0.000 0.000 0.036 0.008
#> GSM152874 1 0.1251 0.93899 0.956 0.000 0.000 0.036 0.008
#> GSM152875 1 0.0324 0.94158 0.992 0.000 0.000 0.004 0.004
#> GSM152876 1 0.0451 0.94064 0.988 0.000 0.004 0.008 0.000
#> GSM152877 1 0.1251 0.93899 0.956 0.000 0.000 0.036 0.008
#> GSM152878 1 0.1251 0.93899 0.956 0.000 0.000 0.036 0.008
#> GSM152879 1 0.1251 0.93899 0.956 0.000 0.000 0.036 0.008
#> GSM152880 1 0.1251 0.93899 0.956 0.000 0.000 0.036 0.008
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.3526 0.59790 0.000 0.792 0.020 0.172 0.000 0.016
#> GSM152805 5 0.2996 0.73717 0.000 0.000 0.228 0.000 0.772 0.000
#> GSM152806 5 0.0146 0.89058 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM152807 2 0.4408 0.57157 0.000 0.656 0.000 0.052 0.000 0.292
#> GSM152808 5 0.0146 0.89058 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM152809 2 0.4751 0.55263 0.000 0.616 0.000 0.072 0.000 0.312
#> GSM152810 5 0.4708 0.77459 0.032 0.004 0.092 0.100 0.760 0.012
#> GSM152811 5 0.0653 0.89072 0.000 0.000 0.012 0.004 0.980 0.004
#> GSM152812 2 0.4686 0.53753 0.000 0.588 0.000 0.044 0.004 0.364
#> GSM152813 2 0.1930 0.64899 0.000 0.916 0.000 0.036 0.000 0.048
#> GSM152814 2 0.1265 0.65250 0.000 0.948 0.000 0.008 0.000 0.044
#> GSM152815 2 0.4675 0.53968 0.000 0.592 0.000 0.044 0.004 0.360
#> GSM152816 3 0.2558 0.73982 0.000 0.104 0.868 0.000 0.000 0.028
#> GSM152817 5 0.0146 0.89058 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM152818 5 0.0458 0.88882 0.000 0.000 0.016 0.000 0.984 0.000
#> GSM152819 2 0.4517 0.06302 0.000 0.524 0.444 0.000 0.000 0.032
#> GSM152820 2 0.4469 -0.00204 0.000 0.504 0.468 0.000 0.000 0.028
#> GSM152821 2 0.2261 0.64635 0.000 0.884 0.104 0.004 0.000 0.008
#> GSM153115 4 0.0000 0.91249 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153116 2 0.4472 -0.02733 0.000 0.496 0.476 0.000 0.000 0.028
#> GSM153117 2 0.4423 0.24211 0.000 0.552 0.420 0.000 0.000 0.028
#> GSM153118 2 0.2312 0.63865 0.000 0.876 0.112 0.000 0.000 0.012
#> GSM153119 5 0.2442 0.82369 0.000 0.000 0.144 0.000 0.852 0.004
#> GSM153120 4 0.0405 0.90987 0.000 0.004 0.000 0.988 0.000 0.008
#> GSM153121 3 0.1265 0.76213 0.000 0.044 0.948 0.000 0.000 0.008
#> GSM153122 5 0.2118 0.85113 0.000 0.000 0.104 0.000 0.888 0.008
#> GSM153123 2 0.2738 0.61689 0.000 0.820 0.176 0.000 0.000 0.004
#> GSM153124 4 0.1845 0.84233 0.000 0.072 0.004 0.916 0.000 0.008
#> GSM153125 4 0.0146 0.91158 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM153126 3 0.0363 0.75081 0.000 0.000 0.988 0.000 0.000 0.012
#> GSM153127 2 0.4686 0.53753 0.000 0.588 0.000 0.044 0.004 0.364
#> GSM153128 3 0.6867 0.39282 0.000 0.304 0.484 0.048 0.136 0.028
#> GSM153129 2 0.3565 0.49152 0.000 0.692 0.304 0.000 0.000 0.004
#> GSM153130 3 0.1267 0.69170 0.000 0.000 0.940 0.000 0.060 0.000
#> GSM153131 3 0.3318 0.70029 0.000 0.172 0.796 0.000 0.000 0.032
#> GSM153132 2 0.4399 0.04883 0.000 0.516 0.460 0.000 0.000 0.024
#> GSM153133 2 0.2703 0.61810 0.000 0.824 0.172 0.000 0.000 0.004
#> GSM153134 2 0.3728 0.44697 0.000 0.652 0.344 0.000 0.000 0.004
#> GSM153135 2 0.4686 0.53753 0.000 0.588 0.000 0.044 0.004 0.364
#> GSM153136 4 0.0000 0.91249 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153137 2 0.5543 0.51597 0.000 0.592 0.004 0.168 0.004 0.232
#> GSM153138 2 0.3776 0.65230 0.000 0.808 0.108 0.052 0.000 0.032
#> GSM153139 3 0.0363 0.75964 0.000 0.012 0.988 0.000 0.000 0.000
#> GSM153140 2 0.1391 0.65357 0.000 0.944 0.000 0.016 0.000 0.040
#> GSM153141 2 0.4686 0.53753 0.000 0.588 0.000 0.044 0.004 0.364
#> GSM153142 3 0.3607 0.25701 0.000 0.000 0.652 0.000 0.348 0.000
#> GSM153143 2 0.3096 0.63159 0.000 0.840 0.004 0.048 0.000 0.108
#> GSM153144 2 0.2277 0.64969 0.000 0.892 0.076 0.000 0.000 0.032
#> GSM153145 5 0.0146 0.89058 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM153146 2 0.2680 0.63736 0.000 0.856 0.124 0.004 0.000 0.016
#> GSM153147 2 0.4051 0.20210 0.000 0.560 0.432 0.000 0.000 0.008
#> GSM153148 2 0.4686 0.53753 0.000 0.588 0.000 0.044 0.004 0.364
#> GSM153149 2 0.3139 0.60305 0.000 0.812 0.160 0.000 0.000 0.028
#> GSM153150 4 0.0000 0.91249 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153151 2 0.3936 0.46008 0.000 0.688 0.288 0.000 0.000 0.024
#> GSM153152 2 0.3714 0.43004 0.000 0.656 0.340 0.000 0.000 0.004
#> GSM153153 2 0.2446 0.63805 0.000 0.864 0.124 0.000 0.000 0.012
#> GSM153154 3 0.3756 0.26701 0.000 0.400 0.600 0.000 0.000 0.000
#> GSM153155 2 0.2449 0.65516 0.000 0.888 0.080 0.020 0.000 0.012
#> GSM153156 3 0.0547 0.76222 0.000 0.020 0.980 0.000 0.000 0.000
#> GSM153157 5 0.2278 0.83860 0.000 0.000 0.128 0.000 0.868 0.004
#> GSM153158 3 0.4123 0.19178 0.000 0.420 0.568 0.000 0.000 0.012
#> GSM153159 3 0.2416 0.56556 0.000 0.000 0.844 0.000 0.156 0.000
#> GSM153160 3 0.0363 0.75081 0.000 0.000 0.988 0.000 0.000 0.012
#> GSM153161 2 0.4675 0.53889 0.000 0.592 0.000 0.044 0.004 0.360
#> GSM153162 3 0.3490 0.59833 0.000 0.268 0.724 0.000 0.000 0.008
#> GSM153163 3 0.0000 0.75416 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM153164 2 0.4029 0.45672 0.000 0.680 0.292 0.000 0.000 0.028
#> GSM153165 3 0.0260 0.75749 0.000 0.008 0.992 0.000 0.000 0.000
#> GSM153166 2 0.3529 0.56939 0.000 0.764 0.208 0.000 0.000 0.028
#> GSM153167 2 0.3468 0.54120 0.000 0.728 0.264 0.000 0.000 0.008
#> GSM153168 5 0.0146 0.89058 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM153169 3 0.1075 0.70757 0.000 0.000 0.952 0.000 0.048 0.000
#> GSM153170 3 0.2664 0.68693 0.000 0.184 0.816 0.000 0.000 0.000
#> GSM153171 4 0.0000 0.91249 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153172 2 0.1036 0.65474 0.000 0.964 0.008 0.004 0.000 0.024
#> GSM153173 3 0.0146 0.75658 0.000 0.004 0.996 0.000 0.000 0.000
#> GSM153174 2 0.3421 0.55777 0.000 0.736 0.256 0.000 0.000 0.008
#> GSM153175 4 0.0000 0.91249 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153176 4 0.3084 0.77397 0.000 0.008 0.136 0.832 0.000 0.024
#> GSM153177 2 0.3409 0.57942 0.000 0.780 0.192 0.000 0.000 0.028
#> GSM152931 4 0.0146 0.91158 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM152932 2 0.2358 0.63945 0.000 0.876 0.108 0.000 0.000 0.016
#> GSM152933 2 0.3345 0.56466 0.000 0.776 0.204 0.000 0.000 0.020
#> GSM152934 4 0.4055 0.65639 0.000 0.136 0.088 0.768 0.000 0.008
#> GSM152935 2 0.3863 0.48117 0.000 0.712 0.260 0.000 0.000 0.028
#> GSM152936 4 0.0000 0.91249 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152937 3 0.6439 0.50862 0.000 0.116 0.576 0.080 0.216 0.012
#> GSM152938 3 0.2615 0.73004 0.000 0.136 0.852 0.008 0.000 0.004
#> GSM152939 4 0.1176 0.89093 0.000 0.000 0.020 0.956 0.000 0.024
#> GSM152940 4 0.0146 0.91190 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM152941 4 0.4393 0.02510 0.480 0.004 0.000 0.500 0.000 0.016
#> GSM152942 3 0.2218 0.74781 0.000 0.104 0.884 0.000 0.000 0.012
#> GSM152943 4 0.5338 -0.21843 0.000 0.444 0.080 0.468 0.000 0.008
#> GSM152944 3 0.0363 0.75964 0.000 0.012 0.988 0.000 0.000 0.000
#> GSM152945 2 0.5060 0.53483 0.000 0.664 0.228 0.084 0.000 0.024
#> GSM152946 2 0.2675 0.64449 0.000 0.876 0.008 0.076 0.000 0.040
#> GSM152947 4 0.0458 0.90940 0.000 0.000 0.000 0.984 0.000 0.016
#> GSM152948 2 0.4616 0.56462 0.000 0.648 0.000 0.072 0.000 0.280
#> GSM152949 3 0.3555 0.58359 0.000 0.280 0.712 0.000 0.000 0.008
#> GSM152950 3 0.3997 0.04896 0.000 0.488 0.508 0.000 0.000 0.004
#> GSM152951 2 0.3830 0.60350 0.000 0.744 0.000 0.044 0.000 0.212
#> GSM152952 2 0.4686 0.53753 0.000 0.588 0.000 0.044 0.004 0.364
#> GSM152953 2 0.4183 0.59572 0.000 0.740 0.000 0.076 0.004 0.180
#> GSM152954 4 0.0000 0.91249 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152955 3 0.5956 0.12847 0.000 0.404 0.464 0.096 0.000 0.036
#> GSM152956 2 0.4686 0.53753 0.000 0.588 0.000 0.044 0.004 0.364
#> GSM152957 4 0.0260 0.91138 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM152958 4 0.0291 0.91078 0.000 0.004 0.000 0.992 0.000 0.004
#> GSM152959 4 0.0260 0.91138 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM152960 4 0.0146 0.91167 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM152961 4 0.0405 0.90993 0.000 0.004 0.000 0.988 0.000 0.008
#> GSM152962 2 0.4456 0.05656 0.000 0.524 0.448 0.000 0.000 0.028
#> GSM152963 2 0.4686 0.53753 0.000 0.588 0.000 0.044 0.004 0.364
#> GSM152964 5 0.6662 0.50983 0.000 0.048 0.208 0.136 0.568 0.040
#> GSM152965 2 0.2933 0.63601 0.000 0.844 0.128 0.016 0.000 0.012
#> GSM152966 4 0.0146 0.91158 0.000 0.000 0.000 0.996 0.000 0.004
#> GSM152967 2 0.2081 0.65322 0.000 0.916 0.012 0.036 0.000 0.036
#> GSM152968 3 0.3851 0.11086 0.000 0.460 0.540 0.000 0.000 0.000
#> GSM152969 4 0.0000 0.91249 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152970 4 0.0458 0.90940 0.000 0.000 0.000 0.984 0.000 0.016
#> GSM152971 4 0.0000 0.91249 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152972 4 0.0000 0.91249 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152973 4 0.3135 0.78018 0.000 0.012 0.124 0.836 0.000 0.028
#> GSM152974 2 0.2039 0.65557 0.000 0.908 0.072 0.004 0.000 0.016
#> GSM152975 2 0.4125 0.62255 0.000 0.764 0.120 0.108 0.000 0.008
#> GSM152976 4 0.0363 0.91063 0.000 0.000 0.000 0.988 0.000 0.012
#> GSM152977 4 0.2540 0.81108 0.000 0.004 0.104 0.872 0.000 0.020
#> GSM152978 4 0.0622 0.90439 0.000 0.012 0.000 0.980 0.000 0.008
#> GSM152979 3 0.0146 0.75671 0.000 0.004 0.996 0.000 0.000 0.000
#> GSM152980 2 0.4735 0.61660 0.000 0.724 0.104 0.144 0.000 0.028
#> GSM152981 5 0.0363 0.89148 0.000 0.000 0.012 0.000 0.988 0.000
#> GSM152982 4 0.0260 0.91127 0.000 0.000 0.000 0.992 0.000 0.008
#> GSM152983 4 0.0000 0.91249 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152984 4 0.6136 0.25837 0.000 0.212 0.240 0.524 0.000 0.024
#> GSM152985 4 0.3767 0.59101 0.260 0.004 0.000 0.720 0.000 0.016
#> GSM152986 4 0.0000 0.91249 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152987 1 0.4370 0.05731 0.536 0.004 0.000 0.444 0.000 0.016
#> GSM152988 4 0.2377 0.83372 0.000 0.008 0.076 0.892 0.000 0.024
#> GSM152989 4 0.0964 0.90067 0.012 0.004 0.000 0.968 0.000 0.016
#> GSM152990 3 0.0458 0.76154 0.000 0.016 0.984 0.000 0.000 0.000
#> GSM152991 2 0.4473 -0.03977 0.000 0.492 0.480 0.000 0.000 0.028
#> GSM187524 1 0.0000 0.51630 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM187525 1 0.0000 0.51630 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM187526 1 0.0000 0.51630 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM187527 1 0.3996 -0.72525 0.512 0.004 0.000 0.000 0.000 0.484
#> GSM152856 6 0.3810 0.97505 0.428 0.000 0.000 0.000 0.000 0.572
#> GSM152857 1 0.4813 0.27724 0.680 0.004 0.004 0.096 0.000 0.216
#> GSM152858 1 0.3409 -0.03040 0.700 0.000 0.000 0.000 0.000 0.300
#> GSM152859 1 0.0146 0.51536 0.996 0.004 0.000 0.000 0.000 0.000
#> GSM152860 1 0.0363 0.51388 0.988 0.000 0.000 0.000 0.000 0.012
#> GSM152861 6 0.3862 0.85368 0.476 0.000 0.000 0.000 0.000 0.524
#> GSM152862 1 0.0632 0.50728 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM152863 1 0.3995 -0.72770 0.516 0.004 0.000 0.000 0.000 0.480
#> GSM152864 6 0.3810 0.97505 0.428 0.000 0.000 0.000 0.000 0.572
#> GSM152865 6 0.3864 0.84081 0.480 0.000 0.000 0.000 0.000 0.520
#> GSM152866 1 0.3101 0.19039 0.756 0.000 0.000 0.000 0.000 0.244
#> GSM152867 6 0.3810 0.97505 0.428 0.000 0.000 0.000 0.000 0.572
#> GSM152868 6 0.3810 0.97505 0.428 0.000 0.000 0.000 0.000 0.572
#> GSM152869 6 0.3810 0.97505 0.428 0.000 0.000 0.000 0.000 0.572
#> GSM152870 1 0.0146 0.51622 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM152871 1 0.3847 -0.65240 0.544 0.000 0.000 0.000 0.000 0.456
#> GSM152872 1 0.3076 0.19696 0.760 0.000 0.000 0.000 0.000 0.240
#> GSM152873 6 0.3810 0.97505 0.428 0.000 0.000 0.000 0.000 0.572
#> GSM152874 6 0.3810 0.97505 0.428 0.000 0.000 0.000 0.000 0.572
#> GSM152875 1 0.3868 -0.76580 0.508 0.000 0.000 0.000 0.000 0.492
#> GSM152876 1 0.3995 -0.72770 0.516 0.004 0.000 0.000 0.000 0.480
#> GSM152877 6 0.3810 0.97505 0.428 0.000 0.000 0.000 0.000 0.572
#> GSM152878 6 0.3810 0.97505 0.428 0.000 0.000 0.000 0.000 0.572
#> GSM152879 6 0.3810 0.97505 0.428 0.000 0.000 0.000 0.000 0.572
#> GSM152880 6 0.3810 0.97505 0.428 0.000 0.000 0.000 0.000 0.572
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> MAD:mclust 169 1.38e-28 2
#> MAD:mclust 165 8.50e-34 3
#> MAD:mclust 164 9.74e-34 4
#> MAD:mclust 159 1.53e-32 5
#> MAD:mclust 137 8.29e-28 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["MAD", "NMF"]
# you can also extract it by
# res = res_list["MAD:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'MAD' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.987 0.964 0.984 0.4731 0.523 0.523
#> 3 3 0.558 0.676 0.847 0.3897 0.689 0.470
#> 4 4 0.537 0.579 0.766 0.1065 0.838 0.593
#> 5 5 0.548 0.494 0.722 0.0758 0.851 0.553
#> 6 6 0.585 0.523 0.715 0.0466 0.881 0.540
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.993 0.000 1.000
#> GSM152805 2 0.0000 0.993 0.000 1.000
#> GSM152806 2 0.0000 0.993 0.000 1.000
#> GSM152807 2 0.0000 0.993 0.000 1.000
#> GSM152808 2 0.0000 0.993 0.000 1.000
#> GSM152809 2 0.0000 0.993 0.000 1.000
#> GSM152810 1 0.2948 0.930 0.948 0.052
#> GSM152811 2 0.0000 0.993 0.000 1.000
#> GSM152812 2 0.0000 0.993 0.000 1.000
#> GSM152813 2 0.0000 0.993 0.000 1.000
#> GSM152814 2 0.0000 0.993 0.000 1.000
#> GSM152815 2 0.0000 0.993 0.000 1.000
#> GSM152816 2 0.0000 0.993 0.000 1.000
#> GSM152817 2 0.0000 0.993 0.000 1.000
#> GSM152818 2 0.0000 0.993 0.000 1.000
#> GSM152819 2 0.0000 0.993 0.000 1.000
#> GSM152820 2 0.0000 0.993 0.000 1.000
#> GSM152821 2 0.0000 0.993 0.000 1.000
#> GSM153115 1 0.0000 0.969 1.000 0.000
#> GSM153116 2 0.0000 0.993 0.000 1.000
#> GSM153117 2 0.0000 0.993 0.000 1.000
#> GSM153118 2 0.0000 0.993 0.000 1.000
#> GSM153119 2 0.0000 0.993 0.000 1.000
#> GSM153120 1 0.0000 0.969 1.000 0.000
#> GSM153121 2 0.0000 0.993 0.000 1.000
#> GSM153122 2 0.0000 0.993 0.000 1.000
#> GSM153123 2 0.0000 0.993 0.000 1.000
#> GSM153124 2 0.8144 0.655 0.252 0.748
#> GSM153125 1 0.4022 0.905 0.920 0.080
#> GSM153126 2 0.0000 0.993 0.000 1.000
#> GSM153127 2 0.0000 0.993 0.000 1.000
#> GSM153128 2 0.0000 0.993 0.000 1.000
#> GSM153129 2 0.0000 0.993 0.000 1.000
#> GSM153130 2 0.0000 0.993 0.000 1.000
#> GSM153131 2 0.0000 0.993 0.000 1.000
#> GSM153132 2 0.0000 0.993 0.000 1.000
#> GSM153133 2 0.0000 0.993 0.000 1.000
#> GSM153134 2 0.0000 0.993 0.000 1.000
#> GSM153135 2 0.0000 0.993 0.000 1.000
#> GSM153136 1 0.0938 0.960 0.988 0.012
#> GSM153137 1 0.5629 0.852 0.868 0.132
#> GSM153138 2 0.0000 0.993 0.000 1.000
#> GSM153139 2 0.0000 0.993 0.000 1.000
#> GSM153140 2 0.0000 0.993 0.000 1.000
#> GSM153141 2 0.0000 0.993 0.000 1.000
#> GSM153142 2 0.0000 0.993 0.000 1.000
#> GSM153143 2 0.0000 0.993 0.000 1.000
#> GSM153144 2 0.0000 0.993 0.000 1.000
#> GSM153145 2 0.0000 0.993 0.000 1.000
#> GSM153146 2 0.0000 0.993 0.000 1.000
#> GSM153147 2 0.0000 0.993 0.000 1.000
#> GSM153148 2 0.0000 0.993 0.000 1.000
#> GSM153149 2 0.0000 0.993 0.000 1.000
#> GSM153150 1 0.0000 0.969 1.000 0.000
#> GSM153151 2 0.0000 0.993 0.000 1.000
#> GSM153152 2 0.0000 0.993 0.000 1.000
#> GSM153153 2 0.0000 0.993 0.000 1.000
#> GSM153154 2 0.0000 0.993 0.000 1.000
#> GSM153155 2 0.0000 0.993 0.000 1.000
#> GSM153156 2 0.0000 0.993 0.000 1.000
#> GSM153157 2 0.0000 0.993 0.000 1.000
#> GSM153158 2 0.0000 0.993 0.000 1.000
#> GSM153159 2 0.0000 0.993 0.000 1.000
#> GSM153160 2 0.0000 0.993 0.000 1.000
#> GSM153161 2 0.0000 0.993 0.000 1.000
#> GSM153162 2 0.0000 0.993 0.000 1.000
#> GSM153163 2 0.0000 0.993 0.000 1.000
#> GSM153164 2 0.0000 0.993 0.000 1.000
#> GSM153165 2 0.0000 0.993 0.000 1.000
#> GSM153166 2 0.0000 0.993 0.000 1.000
#> GSM153167 2 0.0000 0.993 0.000 1.000
#> GSM153168 2 0.0000 0.993 0.000 1.000
#> GSM153169 2 0.0000 0.993 0.000 1.000
#> GSM153170 2 0.0000 0.993 0.000 1.000
#> GSM153171 1 0.0000 0.969 1.000 0.000
#> GSM153172 2 0.0000 0.993 0.000 1.000
#> GSM153173 2 0.0000 0.993 0.000 1.000
#> GSM153174 2 0.0000 0.993 0.000 1.000
#> GSM153175 1 0.7745 0.723 0.772 0.228
#> GSM153176 1 0.8267 0.664 0.740 0.260
#> GSM153177 2 0.0000 0.993 0.000 1.000
#> GSM152931 1 0.6712 0.798 0.824 0.176
#> GSM152932 2 0.0000 0.993 0.000 1.000
#> GSM152933 2 0.0000 0.993 0.000 1.000
#> GSM152934 1 0.9754 0.350 0.592 0.408
#> GSM152935 2 0.0000 0.993 0.000 1.000
#> GSM152936 1 0.0000 0.969 1.000 0.000
#> GSM152937 2 0.0376 0.989 0.004 0.996
#> GSM152938 2 0.0000 0.993 0.000 1.000
#> GSM152939 2 0.6343 0.806 0.160 0.840
#> GSM152940 1 0.0000 0.969 1.000 0.000
#> GSM152941 1 0.0000 0.969 1.000 0.000
#> GSM152942 2 0.0000 0.993 0.000 1.000
#> GSM152943 1 0.5629 0.851 0.868 0.132
#> GSM152944 2 0.0000 0.993 0.000 1.000
#> GSM152945 2 0.1843 0.966 0.028 0.972
#> GSM152946 2 0.0000 0.993 0.000 1.000
#> GSM152947 1 0.0000 0.969 1.000 0.000
#> GSM152948 2 0.0000 0.993 0.000 1.000
#> GSM152949 2 0.0000 0.993 0.000 1.000
#> GSM152950 2 0.0000 0.993 0.000 1.000
#> GSM152951 2 0.0000 0.993 0.000 1.000
#> GSM152952 2 0.3431 0.927 0.064 0.936
#> GSM152953 2 0.0000 0.993 0.000 1.000
#> GSM152954 1 0.0000 0.969 1.000 0.000
#> GSM152955 2 0.0000 0.993 0.000 1.000
#> GSM152956 2 0.0000 0.993 0.000 1.000
#> GSM152957 1 0.0000 0.969 1.000 0.000
#> GSM152958 1 0.0000 0.969 1.000 0.000
#> GSM152959 1 0.0000 0.969 1.000 0.000
#> GSM152960 1 0.0000 0.969 1.000 0.000
#> GSM152961 1 0.0000 0.969 1.000 0.000
#> GSM152962 2 0.0000 0.993 0.000 1.000
#> GSM152963 2 0.0000 0.993 0.000 1.000
#> GSM152964 2 0.6801 0.775 0.180 0.820
#> GSM152965 2 0.0000 0.993 0.000 1.000
#> GSM152966 1 0.3274 0.923 0.940 0.060
#> GSM152967 2 0.0000 0.993 0.000 1.000
#> GSM152968 2 0.0000 0.993 0.000 1.000
#> GSM152969 1 0.0000 0.969 1.000 0.000
#> GSM152970 1 0.0000 0.969 1.000 0.000
#> GSM152971 1 0.2043 0.946 0.968 0.032
#> GSM152972 1 0.0000 0.969 1.000 0.000
#> GSM152973 2 0.1414 0.974 0.020 0.980
#> GSM152974 2 0.0000 0.993 0.000 1.000
#> GSM152975 2 0.0376 0.989 0.004 0.996
#> GSM152976 1 0.0000 0.969 1.000 0.000
#> GSM152977 1 0.2603 0.937 0.956 0.044
#> GSM152978 1 0.0000 0.969 1.000 0.000
#> GSM152979 2 0.0000 0.993 0.000 1.000
#> GSM152980 2 0.1184 0.978 0.016 0.984
#> GSM152981 2 0.0000 0.993 0.000 1.000
#> GSM152982 1 0.9775 0.337 0.588 0.412
#> GSM152983 1 0.0000 0.969 1.000 0.000
#> GSM152984 2 0.0000 0.993 0.000 1.000
#> GSM152985 1 0.0000 0.969 1.000 0.000
#> GSM152986 1 0.0000 0.969 1.000 0.000
#> GSM152987 1 0.0000 0.969 1.000 0.000
#> GSM152988 2 0.1184 0.978 0.016 0.984
#> GSM152989 1 0.0000 0.969 1.000 0.000
#> GSM152990 2 0.0000 0.993 0.000 1.000
#> GSM152991 2 0.0000 0.993 0.000 1.000
#> GSM187524 1 0.0000 0.969 1.000 0.000
#> GSM187525 1 0.0000 0.969 1.000 0.000
#> GSM187526 1 0.0000 0.969 1.000 0.000
#> GSM187527 1 0.0000 0.969 1.000 0.000
#> GSM152856 1 0.0000 0.969 1.000 0.000
#> GSM152857 1 0.0000 0.969 1.000 0.000
#> GSM152858 1 0.0000 0.969 1.000 0.000
#> GSM152859 1 0.0000 0.969 1.000 0.000
#> GSM152860 1 0.0000 0.969 1.000 0.000
#> GSM152861 1 0.0000 0.969 1.000 0.000
#> GSM152862 1 0.0000 0.969 1.000 0.000
#> GSM152863 1 0.0000 0.969 1.000 0.000
#> GSM152864 1 0.0000 0.969 1.000 0.000
#> GSM152865 1 0.0000 0.969 1.000 0.000
#> GSM152866 1 0.0000 0.969 1.000 0.000
#> GSM152867 1 0.0000 0.969 1.000 0.000
#> GSM152868 1 0.0000 0.969 1.000 0.000
#> GSM152869 1 0.0000 0.969 1.000 0.000
#> GSM152870 1 0.0000 0.969 1.000 0.000
#> GSM152871 1 0.0000 0.969 1.000 0.000
#> GSM152872 1 0.0000 0.969 1.000 0.000
#> GSM152873 1 0.0000 0.969 1.000 0.000
#> GSM152874 1 0.0000 0.969 1.000 0.000
#> GSM152875 1 0.0000 0.969 1.000 0.000
#> GSM152876 1 0.0000 0.969 1.000 0.000
#> GSM152877 1 0.0000 0.969 1.000 0.000
#> GSM152878 1 0.0000 0.969 1.000 0.000
#> GSM152879 1 0.0000 0.969 1.000 0.000
#> GSM152880 1 0.0000 0.969 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.2959 0.72597 0.000 0.900 0.100
#> GSM152805 3 0.1753 0.82088 0.048 0.000 0.952
#> GSM152806 3 0.3038 0.79090 0.104 0.000 0.896
#> GSM152807 2 0.0237 0.75321 0.000 0.996 0.004
#> GSM152808 3 0.3340 0.77954 0.120 0.000 0.880
#> GSM152809 2 0.0000 0.75177 0.000 1.000 0.000
#> GSM152810 3 0.6126 0.35146 0.400 0.000 0.600
#> GSM152811 3 0.4654 0.69959 0.208 0.000 0.792
#> GSM152812 2 0.0237 0.75321 0.000 0.996 0.004
#> GSM152813 2 0.2165 0.74536 0.000 0.936 0.064
#> GSM152814 2 0.3551 0.70145 0.000 0.868 0.132
#> GSM152815 2 0.0237 0.75325 0.000 0.996 0.004
#> GSM152816 3 0.0661 0.83558 0.008 0.004 0.988
#> GSM152817 3 0.3482 0.77395 0.128 0.000 0.872
#> GSM152818 3 0.2796 0.79838 0.092 0.000 0.908
#> GSM152819 3 0.1753 0.83229 0.000 0.048 0.952
#> GSM152820 3 0.2066 0.82782 0.000 0.060 0.940
#> GSM152821 2 0.5882 0.39508 0.000 0.652 0.348
#> GSM153115 2 0.3619 0.64416 0.136 0.864 0.000
#> GSM153116 3 0.0424 0.83699 0.000 0.008 0.992
#> GSM153117 3 0.4346 0.74666 0.000 0.184 0.816
#> GSM153118 2 0.6235 0.16351 0.000 0.564 0.436
#> GSM153119 3 0.2625 0.80349 0.084 0.000 0.916
#> GSM153120 1 0.6244 0.38760 0.560 0.440 0.000
#> GSM153121 3 0.1860 0.83084 0.000 0.052 0.948
#> GSM153122 3 0.4399 0.71993 0.188 0.000 0.812
#> GSM153123 2 0.6168 0.23640 0.000 0.588 0.412
#> GSM153124 2 0.1753 0.72759 0.048 0.952 0.000
#> GSM153125 2 0.1753 0.72729 0.048 0.952 0.000
#> GSM153126 3 0.0983 0.83442 0.016 0.004 0.980
#> GSM153127 2 0.0424 0.75387 0.000 0.992 0.008
#> GSM153128 3 0.1411 0.82657 0.036 0.000 0.964
#> GSM153129 3 0.5733 0.56240 0.000 0.324 0.676
#> GSM153130 3 0.0592 0.83395 0.012 0.000 0.988
#> GSM153131 3 0.0424 0.83746 0.000 0.008 0.992
#> GSM153132 3 0.3116 0.80293 0.000 0.108 0.892
#> GSM153133 2 0.6215 0.18810 0.000 0.572 0.428
#> GSM153134 3 0.6062 0.43523 0.000 0.384 0.616
#> GSM153135 2 0.0237 0.75066 0.004 0.996 0.000
#> GSM153136 2 0.5621 0.36010 0.308 0.692 0.000
#> GSM153137 2 0.2066 0.71870 0.060 0.940 0.000
#> GSM153138 2 0.3619 0.70076 0.000 0.864 0.136
#> GSM153139 3 0.0424 0.83706 0.000 0.008 0.992
#> GSM153140 2 0.2537 0.73723 0.000 0.920 0.080
#> GSM153141 2 0.0237 0.75066 0.004 0.996 0.000
#> GSM153142 3 0.0592 0.83395 0.012 0.000 0.988
#> GSM153143 2 0.0983 0.75465 0.004 0.980 0.016
#> GSM153144 2 0.4235 0.66127 0.000 0.824 0.176
#> GSM153145 3 0.2448 0.80771 0.076 0.000 0.924
#> GSM153146 2 0.6204 0.20108 0.000 0.576 0.424
#> GSM153147 3 0.5497 0.61552 0.000 0.292 0.708
#> GSM153148 2 0.1163 0.75352 0.000 0.972 0.028
#> GSM153149 3 0.6244 0.28416 0.000 0.440 0.560
#> GSM153150 1 0.5968 0.54594 0.636 0.364 0.000
#> GSM153151 3 0.4555 0.73120 0.000 0.200 0.800
#> GSM153152 3 0.5810 0.53873 0.000 0.336 0.664
#> GSM153153 2 0.6154 0.24582 0.000 0.592 0.408
#> GSM153154 3 0.1529 0.83360 0.000 0.040 0.960
#> GSM153155 2 0.5529 0.49643 0.000 0.704 0.296
#> GSM153156 3 0.0592 0.83733 0.000 0.012 0.988
#> GSM153157 3 0.2537 0.80583 0.080 0.000 0.920
#> GSM153158 3 0.1643 0.83278 0.000 0.044 0.956
#> GSM153159 3 0.0829 0.83508 0.012 0.004 0.984
#> GSM153160 3 0.0829 0.83508 0.012 0.004 0.984
#> GSM153161 2 0.0237 0.75066 0.004 0.996 0.000
#> GSM153162 3 0.5178 0.66618 0.000 0.256 0.744
#> GSM153163 3 0.0237 0.83643 0.000 0.004 0.996
#> GSM153164 3 0.5327 0.64528 0.000 0.272 0.728
#> GSM153165 3 0.0892 0.83721 0.000 0.020 0.980
#> GSM153166 3 0.6154 0.37320 0.000 0.408 0.592
#> GSM153167 3 0.5810 0.53939 0.000 0.336 0.664
#> GSM153168 3 0.3482 0.77365 0.128 0.000 0.872
#> GSM153169 3 0.0747 0.83275 0.016 0.000 0.984
#> GSM153170 3 0.1964 0.82922 0.000 0.056 0.944
#> GSM153171 2 0.6286 -0.12662 0.464 0.536 0.000
#> GSM153172 2 0.4291 0.65713 0.000 0.820 0.180
#> GSM153173 3 0.0237 0.83643 0.000 0.004 0.996
#> GSM153174 2 0.6252 0.13085 0.000 0.556 0.444
#> GSM153175 2 0.3193 0.68595 0.100 0.896 0.004
#> GSM153176 3 0.5905 0.46316 0.352 0.000 0.648
#> GSM153177 3 0.6126 0.39393 0.000 0.400 0.600
#> GSM152931 2 0.1860 0.72449 0.052 0.948 0.000
#> GSM152932 2 0.6204 0.20017 0.000 0.576 0.424
#> GSM152933 3 0.6026 0.45060 0.000 0.376 0.624
#> GSM152934 2 0.9987 0.14737 0.344 0.348 0.308
#> GSM152935 3 0.4399 0.74391 0.000 0.188 0.812
#> GSM152936 2 0.5621 0.36340 0.308 0.692 0.000
#> GSM152937 3 0.3752 0.76163 0.144 0.000 0.856
#> GSM152938 3 0.1129 0.83825 0.004 0.020 0.976
#> GSM152939 2 0.0983 0.74672 0.016 0.980 0.004
#> GSM152940 1 0.6062 0.51042 0.616 0.384 0.000
#> GSM152941 1 0.4504 0.77919 0.804 0.196 0.000
#> GSM152942 3 0.0892 0.83723 0.000 0.020 0.980
#> GSM152943 2 0.5815 0.37759 0.304 0.692 0.004
#> GSM152944 3 0.1163 0.83605 0.000 0.028 0.972
#> GSM152945 3 0.6422 0.52184 0.016 0.324 0.660
#> GSM152946 2 0.0747 0.75482 0.000 0.984 0.016
#> GSM152947 1 0.3482 0.82973 0.872 0.128 0.000
#> GSM152948 2 0.0237 0.75066 0.004 0.996 0.000
#> GSM152949 3 0.4121 0.75976 0.000 0.168 0.832
#> GSM152950 3 0.3551 0.78758 0.000 0.132 0.868
#> GSM152951 2 0.1163 0.75352 0.000 0.972 0.028
#> GSM152952 2 0.0424 0.74901 0.008 0.992 0.000
#> GSM152953 2 0.0983 0.75449 0.004 0.980 0.016
#> GSM152954 1 0.6235 0.39885 0.564 0.436 0.000
#> GSM152955 3 0.1399 0.83724 0.004 0.028 0.968
#> GSM152956 2 0.0661 0.75355 0.004 0.988 0.008
#> GSM152957 1 0.5058 0.72490 0.756 0.244 0.000
#> GSM152958 1 0.6299 0.28942 0.524 0.476 0.000
#> GSM152959 1 0.4291 0.79503 0.820 0.180 0.000
#> GSM152960 2 0.6267 -0.08417 0.452 0.548 0.000
#> GSM152961 1 0.6126 0.47759 0.600 0.400 0.000
#> GSM152962 3 0.2261 0.82427 0.000 0.068 0.932
#> GSM152963 2 0.0237 0.75321 0.000 0.996 0.004
#> GSM152964 3 0.5254 0.62074 0.264 0.000 0.736
#> GSM152965 2 0.6045 0.32356 0.000 0.620 0.380
#> GSM152966 2 0.2625 0.69768 0.084 0.916 0.000
#> GSM152967 2 0.2711 0.73317 0.000 0.912 0.088
#> GSM152968 3 0.3686 0.78253 0.000 0.140 0.860
#> GSM152969 2 0.4062 0.61009 0.164 0.836 0.000
#> GSM152970 1 0.3941 0.81565 0.844 0.156 0.000
#> GSM152971 2 0.3941 0.62108 0.156 0.844 0.000
#> GSM152972 2 0.5216 0.45709 0.260 0.740 0.000
#> GSM152973 3 0.5681 0.68043 0.016 0.236 0.748
#> GSM152974 2 0.5254 0.54788 0.000 0.736 0.264
#> GSM152975 2 0.5905 0.39679 0.000 0.648 0.352
#> GSM152976 1 0.4206 0.83853 0.872 0.088 0.040
#> GSM152977 1 0.6168 0.20082 0.588 0.000 0.412
#> GSM152978 2 0.6215 0.00124 0.428 0.572 0.000
#> GSM152979 3 0.0237 0.83643 0.000 0.004 0.996
#> GSM152980 2 0.4733 0.64325 0.004 0.800 0.196
#> GSM152981 3 0.2625 0.80327 0.084 0.000 0.916
#> GSM152982 2 0.9460 0.41834 0.240 0.500 0.260
#> GSM152983 2 0.6280 -0.10514 0.460 0.540 0.000
#> GSM152984 3 0.5138 0.67160 0.000 0.252 0.748
#> GSM152985 1 0.3551 0.83197 0.868 0.132 0.000
#> GSM152986 2 0.6180 0.04354 0.416 0.584 0.000
#> GSM152987 1 0.1860 0.86904 0.948 0.052 0.000
#> GSM152988 2 0.2496 0.74931 0.004 0.928 0.068
#> GSM152989 1 0.4346 0.79076 0.816 0.184 0.000
#> GSM152990 3 0.0424 0.83699 0.000 0.008 0.992
#> GSM152991 3 0.0892 0.83784 0.000 0.020 0.980
#> GSM187524 1 0.0237 0.85885 0.996 0.000 0.004
#> GSM187525 1 0.0424 0.86399 0.992 0.008 0.000
#> GSM187526 1 0.0747 0.86617 0.984 0.016 0.000
#> GSM187527 1 0.1643 0.86881 0.956 0.044 0.000
#> GSM152856 1 0.2959 0.85160 0.900 0.100 0.000
#> GSM152857 1 0.4121 0.70068 0.832 0.000 0.168
#> GSM152858 1 0.0237 0.85915 0.996 0.000 0.004
#> GSM152859 1 0.1529 0.83281 0.960 0.000 0.040
#> GSM152860 1 0.0424 0.86399 0.992 0.008 0.000
#> GSM152861 1 0.1753 0.86870 0.952 0.048 0.000
#> GSM152862 1 0.0237 0.85915 0.996 0.000 0.004
#> GSM152863 1 0.0592 0.85372 0.988 0.000 0.012
#> GSM152864 1 0.2165 0.86666 0.936 0.064 0.000
#> GSM152865 1 0.0000 0.86078 1.000 0.000 0.000
#> GSM152866 1 0.0237 0.85915 0.996 0.000 0.004
#> GSM152867 1 0.2356 0.86439 0.928 0.072 0.000
#> GSM152868 1 0.2711 0.85757 0.912 0.088 0.000
#> GSM152869 1 0.2261 0.86574 0.932 0.068 0.000
#> GSM152870 1 0.0237 0.85915 0.996 0.000 0.004
#> GSM152871 1 0.0000 0.86078 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.86078 1.000 0.000 0.000
#> GSM152873 1 0.0892 0.86679 0.980 0.020 0.000
#> GSM152874 1 0.1289 0.86795 0.968 0.032 0.000
#> GSM152875 1 0.0237 0.86254 0.996 0.004 0.000
#> GSM152876 1 0.0747 0.86631 0.984 0.016 0.000
#> GSM152877 1 0.1964 0.86816 0.944 0.056 0.000
#> GSM152878 1 0.2066 0.86746 0.940 0.060 0.000
#> GSM152879 1 0.2356 0.86439 0.928 0.072 0.000
#> GSM152880 1 0.2261 0.86577 0.932 0.068 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.5944 0.6752 0.044 0.748 0.116 0.092
#> GSM152805 3 0.1118 0.7285 0.000 0.000 0.964 0.036
#> GSM152806 3 0.2408 0.6920 0.000 0.000 0.896 0.104
#> GSM152807 2 0.1356 0.7788 0.000 0.960 0.008 0.032
#> GSM152808 3 0.3402 0.6426 0.004 0.000 0.832 0.164
#> GSM152809 2 0.0779 0.7798 0.004 0.980 0.000 0.016
#> GSM152810 4 0.6163 0.4211 0.060 0.000 0.364 0.576
#> GSM152811 3 0.3810 0.6134 0.008 0.000 0.804 0.188
#> GSM152812 2 0.0672 0.7802 0.008 0.984 0.000 0.008
#> GSM152813 2 0.2546 0.7700 0.000 0.912 0.028 0.060
#> GSM152814 2 0.2224 0.7741 0.000 0.928 0.040 0.032
#> GSM152815 2 0.1059 0.7791 0.016 0.972 0.000 0.012
#> GSM152816 3 0.1118 0.7366 0.000 0.000 0.964 0.036
#> GSM152817 3 0.3208 0.6571 0.004 0.000 0.848 0.148
#> GSM152818 3 0.1557 0.7161 0.000 0.000 0.944 0.056
#> GSM152819 3 0.3312 0.7149 0.000 0.072 0.876 0.052
#> GSM152820 3 0.3216 0.7107 0.000 0.044 0.880 0.076
#> GSM152821 2 0.1452 0.7776 0.000 0.956 0.036 0.008
#> GSM153115 1 0.7554 0.3001 0.488 0.268 0.000 0.244
#> GSM153116 3 0.3840 0.6829 0.000 0.052 0.844 0.104
#> GSM153117 3 0.4050 0.6769 0.000 0.168 0.808 0.024
#> GSM153118 2 0.2593 0.7627 0.000 0.904 0.080 0.016
#> GSM153119 3 0.4040 0.5586 0.000 0.000 0.752 0.248
#> GSM153120 2 0.6992 0.3562 0.156 0.564 0.000 0.280
#> GSM153121 3 0.4485 0.6792 0.000 0.012 0.740 0.248
#> GSM153122 3 0.4511 0.5057 0.008 0.000 0.724 0.268
#> GSM153123 2 0.5613 0.6424 0.000 0.724 0.156 0.120
#> GSM153124 2 0.7258 0.5309 0.164 0.596 0.016 0.224
#> GSM153125 2 0.5835 0.6506 0.160 0.716 0.004 0.120
#> GSM153126 3 0.4482 0.6687 0.008 0.000 0.728 0.264
#> GSM153127 2 0.1610 0.7757 0.016 0.952 0.000 0.032
#> GSM153128 4 0.5696 0.0899 0.000 0.024 0.484 0.492
#> GSM153129 3 0.6754 0.5822 0.000 0.204 0.612 0.184
#> GSM153130 3 0.2053 0.7399 0.000 0.004 0.924 0.072
#> GSM153131 3 0.1576 0.7413 0.000 0.004 0.948 0.048
#> GSM153132 3 0.2845 0.7238 0.000 0.076 0.896 0.028
#> GSM153133 2 0.3308 0.7521 0.000 0.872 0.092 0.036
#> GSM153134 3 0.6461 0.5858 0.000 0.216 0.640 0.144
#> GSM153135 2 0.0927 0.7784 0.008 0.976 0.000 0.016
#> GSM153136 2 0.6214 0.3670 0.360 0.576 0.000 0.064
#> GSM153137 2 0.2596 0.7596 0.024 0.908 0.000 0.068
#> GSM153138 2 0.4928 0.6841 0.016 0.768 0.028 0.188
#> GSM153139 3 0.1767 0.7418 0.000 0.012 0.944 0.044
#> GSM153140 2 0.2926 0.7645 0.000 0.896 0.048 0.056
#> GSM153141 2 0.1182 0.7767 0.016 0.968 0.000 0.016
#> GSM153142 3 0.1792 0.7138 0.000 0.000 0.932 0.068
#> GSM153143 2 0.0592 0.7801 0.000 0.984 0.000 0.016
#> GSM153144 2 0.4458 0.7163 0.000 0.808 0.076 0.116
#> GSM153145 3 0.3123 0.6585 0.000 0.000 0.844 0.156
#> GSM153146 2 0.2996 0.7622 0.000 0.892 0.064 0.044
#> GSM153147 3 0.6941 0.5715 0.000 0.192 0.588 0.220
#> GSM153148 2 0.0657 0.7797 0.004 0.984 0.000 0.012
#> GSM153149 2 0.3907 0.7129 0.000 0.828 0.140 0.032
#> GSM153150 2 0.7818 -0.0389 0.356 0.388 0.000 0.256
#> GSM153151 2 0.7587 0.2185 0.000 0.476 0.292 0.232
#> GSM153152 3 0.6845 0.1254 0.000 0.448 0.452 0.100
#> GSM153153 2 0.2635 0.7617 0.000 0.904 0.076 0.020
#> GSM153154 3 0.1406 0.7404 0.000 0.024 0.960 0.016
#> GSM153155 2 0.1767 0.7781 0.000 0.944 0.044 0.012
#> GSM153156 3 0.2741 0.7407 0.000 0.012 0.892 0.096
#> GSM153157 3 0.3266 0.6488 0.000 0.000 0.832 0.168
#> GSM153158 3 0.1724 0.7360 0.000 0.032 0.948 0.020
#> GSM153159 3 0.1118 0.7235 0.000 0.000 0.964 0.036
#> GSM153160 3 0.4283 0.6744 0.004 0.000 0.740 0.256
#> GSM153161 2 0.1256 0.7779 0.008 0.964 0.000 0.028
#> GSM153162 3 0.5901 0.6249 0.000 0.068 0.652 0.280
#> GSM153163 3 0.2266 0.7391 0.000 0.004 0.912 0.084
#> GSM153164 2 0.5673 0.1085 0.000 0.528 0.448 0.024
#> GSM153165 3 0.4711 0.6839 0.000 0.024 0.740 0.236
#> GSM153166 3 0.6108 0.2713 0.000 0.424 0.528 0.048
#> GSM153167 3 0.7084 0.4964 0.000 0.284 0.552 0.164
#> GSM153168 3 0.3831 0.6015 0.004 0.000 0.792 0.204
#> GSM153169 3 0.1211 0.7277 0.000 0.000 0.960 0.040
#> GSM153170 3 0.3910 0.7231 0.000 0.024 0.820 0.156
#> GSM153171 1 0.5727 0.5123 0.704 0.200 0.000 0.096
#> GSM153172 2 0.1929 0.7746 0.000 0.940 0.036 0.024
#> GSM153173 3 0.3545 0.7184 0.000 0.008 0.828 0.164
#> GSM153174 3 0.7812 0.2919 0.000 0.328 0.408 0.264
#> GSM153175 1 0.6529 0.4037 0.592 0.084 0.004 0.320
#> GSM153176 3 0.7397 0.3005 0.292 0.000 0.508 0.200
#> GSM153177 2 0.4983 0.5682 0.000 0.704 0.272 0.024
#> GSM152931 2 0.5893 0.6535 0.128 0.712 0.004 0.156
#> GSM152932 2 0.3606 0.7240 0.000 0.844 0.132 0.024
#> GSM152933 2 0.5182 0.5447 0.000 0.684 0.288 0.028
#> GSM152934 4 0.8371 0.1243 0.112 0.360 0.072 0.456
#> GSM152935 3 0.7200 0.2220 0.000 0.372 0.484 0.144
#> GSM152936 2 0.5160 0.6329 0.180 0.748 0.000 0.072
#> GSM152937 4 0.5980 0.2327 0.020 0.012 0.436 0.532
#> GSM152938 3 0.3969 0.7184 0.000 0.016 0.804 0.180
#> GSM152939 1 0.8165 0.2170 0.412 0.256 0.012 0.320
#> GSM152940 2 0.7746 0.0813 0.272 0.440 0.000 0.288
#> GSM152941 1 0.6292 0.3279 0.592 0.076 0.000 0.332
#> GSM152942 3 0.4856 0.6606 0.008 0.008 0.712 0.272
#> GSM152943 2 0.6339 0.3863 0.040 0.580 0.016 0.364
#> GSM152944 3 0.2522 0.7416 0.000 0.016 0.908 0.076
#> GSM152945 4 0.8167 0.2109 0.024 0.324 0.196 0.456
#> GSM152946 2 0.2021 0.7756 0.000 0.936 0.024 0.040
#> GSM152947 1 0.6292 0.1571 0.524 0.060 0.000 0.416
#> GSM152948 2 0.0921 0.7793 0.000 0.972 0.000 0.028
#> GSM152949 3 0.5508 0.6552 0.000 0.056 0.692 0.252
#> GSM152950 3 0.4491 0.6865 0.000 0.140 0.800 0.060
#> GSM152951 2 0.0592 0.7799 0.000 0.984 0.000 0.016
#> GSM152952 2 0.1488 0.7768 0.012 0.956 0.000 0.032
#> GSM152953 2 0.2125 0.7737 0.012 0.932 0.004 0.052
#> GSM152954 2 0.7454 0.1028 0.376 0.448 0.000 0.176
#> GSM152955 3 0.6554 0.1249 0.000 0.084 0.540 0.376
#> GSM152956 2 0.0779 0.7796 0.004 0.980 0.000 0.016
#> GSM152957 1 0.3324 0.6737 0.852 0.012 0.000 0.136
#> GSM152958 2 0.6844 0.0442 0.444 0.456 0.000 0.100
#> GSM152959 1 0.5524 0.4799 0.676 0.048 0.000 0.276
#> GSM152960 2 0.6116 0.5419 0.112 0.668 0.000 0.220
#> GSM152961 1 0.5723 0.4720 0.696 0.220 0.000 0.084
#> GSM152962 3 0.5063 0.6343 0.000 0.124 0.768 0.108
#> GSM152963 2 0.1798 0.7749 0.016 0.944 0.000 0.040
#> GSM152964 4 0.5937 0.3505 0.032 0.004 0.404 0.560
#> GSM152965 2 0.5100 0.6876 0.004 0.768 0.076 0.152
#> GSM152966 2 0.5889 0.6023 0.212 0.688 0.000 0.100
#> GSM152967 2 0.1004 0.7786 0.000 0.972 0.004 0.024
#> GSM152968 3 0.4362 0.7183 0.000 0.096 0.816 0.088
#> GSM152969 2 0.4017 0.7184 0.128 0.828 0.000 0.044
#> GSM152970 1 0.5393 0.4971 0.688 0.044 0.000 0.268
#> GSM152971 2 0.4872 0.6893 0.148 0.776 0.000 0.076
#> GSM152972 2 0.4440 0.6890 0.136 0.804 0.000 0.060
#> GSM152973 1 0.7516 0.1922 0.472 0.000 0.200 0.328
#> GSM152974 2 0.2466 0.7676 0.000 0.916 0.056 0.028
#> GSM152975 2 0.4570 0.6908 0.012 0.784 0.184 0.020
#> GSM152976 1 0.2408 0.7044 0.920 0.004 0.016 0.060
#> GSM152977 4 0.6619 0.4604 0.100 0.000 0.332 0.568
#> GSM152978 2 0.5434 0.6199 0.084 0.728 0.000 0.188
#> GSM152979 3 0.2805 0.7376 0.000 0.012 0.888 0.100
#> GSM152980 2 0.3994 0.7283 0.004 0.828 0.028 0.140
#> GSM152981 3 0.4331 0.4931 0.000 0.000 0.712 0.288
#> GSM152982 2 0.7874 0.5488 0.144 0.592 0.068 0.196
#> GSM152983 2 0.6529 0.4262 0.320 0.592 0.004 0.084
#> GSM152984 3 0.5646 0.6391 0.000 0.056 0.672 0.272
#> GSM152985 4 0.6299 0.1036 0.420 0.060 0.000 0.520
#> GSM152986 1 0.6376 0.0714 0.504 0.432 0.000 0.064
#> GSM152987 4 0.5959 0.1863 0.388 0.044 0.000 0.568
#> GSM152988 1 0.6405 0.3878 0.592 0.028 0.032 0.348
#> GSM152989 1 0.2741 0.6933 0.892 0.012 0.000 0.096
#> GSM152990 3 0.2859 0.7351 0.000 0.008 0.880 0.112
#> GSM152991 3 0.5662 0.5118 0.000 0.072 0.692 0.236
#> GSM187524 4 0.5244 0.1141 0.436 0.008 0.000 0.556
#> GSM187525 4 0.5685 0.0149 0.460 0.024 0.000 0.516
#> GSM187526 1 0.4819 0.4116 0.652 0.004 0.000 0.344
#> GSM187527 1 0.1211 0.7107 0.960 0.000 0.000 0.040
#> GSM152856 1 0.0895 0.7163 0.976 0.004 0.000 0.020
#> GSM152857 1 0.2675 0.6818 0.908 0.000 0.044 0.048
#> GSM152858 1 0.3764 0.6076 0.784 0.000 0.000 0.216
#> GSM152859 4 0.5700 0.1598 0.412 0.000 0.028 0.560
#> GSM152860 1 0.5244 0.1935 0.556 0.008 0.000 0.436
#> GSM152861 1 0.2530 0.6808 0.888 0.000 0.000 0.112
#> GSM152862 1 0.5119 0.1903 0.556 0.004 0.000 0.440
#> GSM152863 1 0.1637 0.7114 0.940 0.000 0.000 0.060
#> GSM152864 1 0.0469 0.7161 0.988 0.000 0.000 0.012
#> GSM152865 1 0.1792 0.7094 0.932 0.000 0.000 0.068
#> GSM152866 1 0.4164 0.5347 0.736 0.000 0.000 0.264
#> GSM152867 1 0.1305 0.7113 0.960 0.004 0.000 0.036
#> GSM152868 1 0.1305 0.7115 0.960 0.004 0.000 0.036
#> GSM152869 1 0.0592 0.7146 0.984 0.000 0.000 0.016
#> GSM152870 1 0.4977 0.1351 0.540 0.000 0.000 0.460
#> GSM152871 1 0.2704 0.6852 0.876 0.000 0.000 0.124
#> GSM152872 1 0.4008 0.5711 0.756 0.000 0.000 0.244
#> GSM152873 1 0.0817 0.7149 0.976 0.000 0.000 0.024
#> GSM152874 1 0.1022 0.7151 0.968 0.000 0.000 0.032
#> GSM152875 1 0.0707 0.7160 0.980 0.000 0.000 0.020
#> GSM152876 1 0.2125 0.6957 0.920 0.004 0.000 0.076
#> GSM152877 1 0.1305 0.7128 0.960 0.004 0.000 0.036
#> GSM152878 1 0.1022 0.7127 0.968 0.000 0.000 0.032
#> GSM152879 1 0.0376 0.7168 0.992 0.004 0.000 0.004
#> GSM152880 1 0.1576 0.7097 0.948 0.004 0.000 0.048
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.7337 0.44936 0.060 0.568 0.240 0.092 0.040
#> GSM152805 3 0.2005 0.66182 0.000 0.004 0.924 0.056 0.016
#> GSM152806 3 0.0771 0.67089 0.000 0.000 0.976 0.004 0.020
#> GSM152807 2 0.0566 0.73615 0.004 0.984 0.000 0.000 0.012
#> GSM152808 3 0.1670 0.66632 0.000 0.000 0.936 0.012 0.052
#> GSM152809 2 0.0671 0.73603 0.004 0.980 0.000 0.000 0.016
#> GSM152810 5 0.5408 0.43642 0.040 0.000 0.248 0.040 0.672
#> GSM152811 3 0.3777 0.60725 0.004 0.000 0.784 0.020 0.192
#> GSM152812 2 0.0981 0.73438 0.008 0.972 0.008 0.000 0.012
#> GSM152813 2 0.2150 0.73175 0.004 0.928 0.020 0.016 0.032
#> GSM152814 2 0.2852 0.72208 0.008 0.892 0.064 0.012 0.024
#> GSM152815 2 0.1314 0.73513 0.012 0.960 0.012 0.000 0.016
#> GSM152816 3 0.3585 0.64544 0.012 0.040 0.856 0.076 0.016
#> GSM152817 3 0.2110 0.65902 0.000 0.000 0.912 0.016 0.072
#> GSM152818 3 0.1300 0.66852 0.000 0.000 0.956 0.028 0.016
#> GSM152819 3 0.4068 0.60116 0.004 0.152 0.800 0.024 0.020
#> GSM152820 3 0.4526 0.63227 0.000 0.080 0.796 0.060 0.064
#> GSM152821 2 0.3879 0.64708 0.000 0.784 0.188 0.012 0.016
#> GSM153115 4 0.7846 -0.04299 0.324 0.192 0.000 0.396 0.088
#> GSM153116 3 0.3683 0.62825 0.000 0.080 0.844 0.044 0.032
#> GSM153117 3 0.3988 0.56858 0.000 0.192 0.776 0.024 0.008
#> GSM153118 2 0.3521 0.66880 0.000 0.808 0.172 0.008 0.012
#> GSM153119 3 0.4617 0.54855 0.000 0.000 0.716 0.060 0.224
#> GSM153120 2 0.6290 0.20356 0.040 0.492 0.000 0.060 0.408
#> GSM153121 4 0.4152 0.52110 0.000 0.000 0.296 0.692 0.012
#> GSM153122 3 0.6391 0.24280 0.004 0.000 0.480 0.152 0.364
#> GSM153123 2 0.5906 0.21933 0.000 0.512 0.064 0.408 0.016
#> GSM153124 4 0.6796 0.16338 0.092 0.296 0.000 0.544 0.068
#> GSM153125 2 0.7219 0.43259 0.180 0.556 0.000 0.164 0.100
#> GSM153126 4 0.3957 0.53342 0.000 0.000 0.280 0.712 0.008
#> GSM153127 2 0.1947 0.73739 0.004 0.932 0.004 0.016 0.044
#> GSM153128 5 0.5905 0.23361 0.000 0.004 0.336 0.104 0.556
#> GSM153129 4 0.6213 0.41797 0.000 0.100 0.324 0.556 0.020
#> GSM153130 3 0.4235 0.35989 0.000 0.000 0.656 0.336 0.008
#> GSM153131 3 0.3085 0.64441 0.008 0.008 0.868 0.100 0.016
#> GSM153132 3 0.3511 0.65528 0.000 0.072 0.848 0.068 0.012
#> GSM153133 2 0.5240 0.60779 0.000 0.688 0.020 0.232 0.060
#> GSM153134 3 0.6548 0.18891 0.000 0.152 0.524 0.308 0.016
#> GSM153135 2 0.1082 0.73690 0.000 0.964 0.000 0.008 0.028
#> GSM153136 2 0.7786 0.31575 0.112 0.464 0.000 0.248 0.176
#> GSM153137 2 0.2301 0.72899 0.004 0.912 0.004 0.016 0.064
#> GSM153138 2 0.3817 0.70154 0.000 0.820 0.032 0.020 0.128
#> GSM153139 3 0.3707 0.55206 0.000 0.004 0.768 0.220 0.008
#> GSM153140 2 0.5159 0.66842 0.016 0.764 0.096 0.088 0.036
#> GSM153141 2 0.0865 0.73592 0.000 0.972 0.000 0.004 0.024
#> GSM153142 3 0.2228 0.66545 0.000 0.000 0.912 0.040 0.048
#> GSM153143 2 0.2654 0.72052 0.000 0.884 0.000 0.032 0.084
#> GSM153144 2 0.3613 0.68617 0.000 0.812 0.016 0.160 0.012
#> GSM153145 3 0.1571 0.66453 0.000 0.000 0.936 0.004 0.060
#> GSM153146 2 0.3059 0.69974 0.000 0.856 0.120 0.008 0.016
#> GSM153147 4 0.4777 0.58374 0.000 0.064 0.188 0.736 0.012
#> GSM153148 2 0.0510 0.73593 0.000 0.984 0.000 0.000 0.016
#> GSM153149 2 0.3455 0.70050 0.000 0.844 0.112 0.024 0.020
#> GSM153150 5 0.7402 0.21229 0.116 0.328 0.000 0.092 0.464
#> GSM153151 2 0.8280 -0.10276 0.000 0.324 0.136 0.216 0.324
#> GSM153152 2 0.6799 0.03899 0.000 0.444 0.168 0.372 0.016
#> GSM153153 2 0.4364 0.59903 0.000 0.740 0.224 0.016 0.020
#> GSM153154 3 0.3866 0.59315 0.000 0.024 0.780 0.192 0.004
#> GSM153155 2 0.1503 0.73524 0.000 0.952 0.020 0.008 0.020
#> GSM153156 3 0.4892 -0.11772 0.000 0.004 0.492 0.488 0.016
#> GSM153157 3 0.4201 0.59823 0.000 0.000 0.752 0.044 0.204
#> GSM153158 3 0.2227 0.66815 0.000 0.048 0.916 0.032 0.004
#> GSM153159 3 0.3327 0.61621 0.000 0.000 0.828 0.144 0.028
#> GSM153160 4 0.3967 0.54479 0.000 0.000 0.264 0.724 0.012
#> GSM153161 2 0.1626 0.73311 0.000 0.940 0.000 0.016 0.044
#> GSM153162 4 0.4121 0.53961 0.000 0.012 0.264 0.720 0.004
#> GSM153163 3 0.3209 0.59565 0.000 0.000 0.812 0.180 0.008
#> GSM153164 3 0.5005 0.43961 0.000 0.300 0.656 0.020 0.024
#> GSM153165 3 0.4686 0.22212 0.000 0.004 0.588 0.396 0.012
#> GSM153166 3 0.5492 0.38278 0.000 0.328 0.608 0.044 0.020
#> GSM153167 4 0.6864 0.38216 0.000 0.236 0.256 0.492 0.016
#> GSM153168 3 0.3675 0.60458 0.000 0.000 0.788 0.024 0.188
#> GSM153169 3 0.4801 0.43193 0.000 0.000 0.668 0.284 0.048
#> GSM153170 4 0.4796 0.19109 0.000 0.008 0.452 0.532 0.008
#> GSM153171 1 0.7849 0.09184 0.384 0.112 0.000 0.356 0.148
#> GSM153172 2 0.1716 0.73627 0.000 0.944 0.016 0.024 0.016
#> GSM153173 3 0.4420 0.09210 0.000 0.000 0.548 0.448 0.004
#> GSM153174 4 0.4545 0.55442 0.004 0.156 0.084 0.756 0.000
#> GSM153175 4 0.4387 0.48380 0.116 0.040 0.000 0.796 0.048
#> GSM153176 4 0.5604 0.57359 0.048 0.000 0.136 0.708 0.108
#> GSM153177 2 0.4107 0.64082 0.000 0.772 0.192 0.016 0.020
#> GSM152931 2 0.6858 0.38825 0.056 0.504 0.000 0.340 0.100
#> GSM152932 2 0.2998 0.72478 0.000 0.884 0.052 0.036 0.028
#> GSM152933 3 0.5099 -0.04451 0.000 0.484 0.488 0.012 0.016
#> GSM152934 5 0.5763 0.50304 0.004 0.120 0.036 0.144 0.696
#> GSM152935 2 0.8404 0.00439 0.000 0.356 0.200 0.188 0.256
#> GSM152936 2 0.6380 0.34768 0.012 0.528 0.000 0.136 0.324
#> GSM152937 5 0.6688 0.24862 0.012 0.004 0.180 0.276 0.528
#> GSM152938 4 0.5024 0.54332 0.000 0.016 0.232 0.700 0.052
#> GSM152939 4 0.4528 0.50464 0.092 0.076 0.000 0.792 0.040
#> GSM152940 5 0.6074 0.30185 0.032 0.300 0.000 0.076 0.592
#> GSM152941 5 0.6226 0.04334 0.400 0.040 0.000 0.056 0.504
#> GSM152942 4 0.3628 0.57831 0.000 0.000 0.216 0.772 0.012
#> GSM152943 5 0.6086 0.08357 0.004 0.392 0.012 0.076 0.516
#> GSM152944 3 0.3143 0.57815 0.000 0.000 0.796 0.204 0.000
#> GSM152945 5 0.6725 0.46293 0.000 0.188 0.100 0.104 0.608
#> GSM152946 2 0.4252 0.67876 0.000 0.768 0.004 0.176 0.052
#> GSM152947 5 0.5612 0.50062 0.096 0.008 0.012 0.204 0.680
#> GSM152948 2 0.0693 0.73668 0.000 0.980 0.000 0.008 0.012
#> GSM152949 4 0.4502 0.49430 0.000 0.012 0.312 0.668 0.008
#> GSM152950 4 0.7410 0.03357 0.000 0.148 0.392 0.396 0.064
#> GSM152951 2 0.1300 0.73540 0.000 0.956 0.000 0.016 0.028
#> GSM152952 2 0.1443 0.73382 0.000 0.948 0.004 0.004 0.044
#> GSM152953 2 0.1569 0.73727 0.000 0.944 0.008 0.004 0.044
#> GSM152954 2 0.8236 -0.19373 0.280 0.308 0.000 0.112 0.300
#> GSM152955 5 0.6230 0.22306 0.000 0.060 0.372 0.040 0.528
#> GSM152956 2 0.0671 0.73591 0.000 0.980 0.004 0.000 0.016
#> GSM152957 4 0.6432 -0.19786 0.372 0.004 0.000 0.468 0.156
#> GSM152958 2 0.7941 0.09842 0.272 0.416 0.000 0.100 0.212
#> GSM152959 5 0.6622 0.27161 0.272 0.036 0.000 0.132 0.560
#> GSM152960 2 0.5167 0.44581 0.016 0.616 0.000 0.028 0.340
#> GSM152961 1 0.7880 0.09883 0.452 0.220 0.000 0.112 0.216
#> GSM152962 4 0.8288 0.12567 0.000 0.136 0.272 0.356 0.236
#> GSM152963 2 0.1413 0.73561 0.000 0.956 0.012 0.012 0.020
#> GSM152964 5 0.5504 0.44307 0.020 0.004 0.240 0.064 0.672
#> GSM152965 2 0.6079 0.54363 0.000 0.644 0.052 0.084 0.220
#> GSM152966 2 0.7213 0.41462 0.176 0.540 0.000 0.208 0.076
#> GSM152967 2 0.2522 0.73436 0.000 0.896 0.004 0.076 0.024
#> GSM152968 3 0.5452 0.14349 0.000 0.056 0.556 0.384 0.004
#> GSM152969 2 0.6962 0.46767 0.120 0.588 0.000 0.112 0.180
#> GSM152970 5 0.6597 0.13167 0.340 0.020 0.000 0.136 0.504
#> GSM152971 2 0.6520 0.50014 0.032 0.580 0.000 0.244 0.144
#> GSM152972 2 0.4985 0.60679 0.012 0.720 0.000 0.076 0.192
#> GSM152973 4 0.4386 0.55530 0.132 0.000 0.056 0.788 0.024
#> GSM152974 2 0.2026 0.73616 0.000 0.928 0.016 0.044 0.012
#> GSM152975 2 0.4851 0.66038 0.000 0.744 0.168 0.020 0.068
#> GSM152976 1 0.6748 0.17850 0.432 0.000 0.020 0.404 0.144
#> GSM152977 5 0.6281 0.48277 0.088 0.000 0.216 0.064 0.632
#> GSM152978 2 0.5963 0.44412 0.036 0.596 0.000 0.060 0.308
#> GSM152979 4 0.4682 0.29264 0.000 0.000 0.420 0.564 0.016
#> GSM152980 2 0.6080 0.54618 0.008 0.656 0.060 0.056 0.220
#> GSM152981 3 0.5285 0.36639 0.000 0.000 0.584 0.060 0.356
#> GSM152982 4 0.6595 0.20431 0.012 0.116 0.016 0.548 0.308
#> GSM152983 5 0.7829 0.12136 0.048 0.288 0.008 0.260 0.396
#> GSM152984 4 0.3504 0.59326 0.000 0.008 0.160 0.816 0.016
#> GSM152985 5 0.3646 0.50968 0.100 0.012 0.000 0.052 0.836
#> GSM152986 2 0.8015 0.19025 0.244 0.436 0.000 0.140 0.180
#> GSM152987 5 0.3837 0.51323 0.116 0.012 0.008 0.036 0.828
#> GSM152988 4 0.4270 0.47654 0.204 0.004 0.016 0.760 0.016
#> GSM152989 1 0.5743 0.51128 0.636 0.008 0.000 0.124 0.232
#> GSM152990 4 0.4467 0.43888 0.000 0.000 0.344 0.640 0.016
#> GSM152991 3 0.5948 0.53055 0.000 0.088 0.676 0.064 0.172
#> GSM187524 5 0.4444 0.34833 0.264 0.000 0.012 0.016 0.708
#> GSM187525 5 0.4986 0.20357 0.336 0.000 0.004 0.036 0.624
#> GSM187526 1 0.5064 0.33663 0.552 0.000 0.004 0.028 0.416
#> GSM187527 1 0.1485 0.76072 0.948 0.000 0.000 0.032 0.020
#> GSM152856 1 0.0865 0.76953 0.972 0.000 0.000 0.004 0.024
#> GSM152857 1 0.2537 0.72917 0.904 0.000 0.056 0.024 0.016
#> GSM152858 1 0.4301 0.60168 0.712 0.000 0.000 0.028 0.260
#> GSM152859 5 0.4802 0.38336 0.240 0.000 0.036 0.016 0.708
#> GSM152860 1 0.5233 0.14963 0.488 0.000 0.008 0.028 0.476
#> GSM152861 1 0.2909 0.71861 0.848 0.000 0.000 0.012 0.140
#> GSM152862 1 0.5225 0.21218 0.508 0.000 0.008 0.028 0.456
#> GSM152863 1 0.2153 0.76901 0.916 0.000 0.000 0.040 0.044
#> GSM152864 1 0.1364 0.77183 0.952 0.000 0.000 0.012 0.036
#> GSM152865 1 0.2233 0.75918 0.904 0.000 0.000 0.016 0.080
#> GSM152866 1 0.4178 0.57079 0.696 0.000 0.008 0.004 0.292
#> GSM152867 1 0.1041 0.76442 0.964 0.000 0.000 0.032 0.004
#> GSM152868 1 0.1082 0.76696 0.964 0.000 0.000 0.028 0.008
#> GSM152869 1 0.1216 0.77107 0.960 0.000 0.000 0.020 0.020
#> GSM152870 5 0.5272 -0.05882 0.432 0.000 0.008 0.032 0.528
#> GSM152871 1 0.3445 0.71005 0.824 0.000 0.000 0.036 0.140
#> GSM152872 1 0.4735 0.53950 0.668 0.000 0.004 0.032 0.296
#> GSM152873 1 0.1809 0.77034 0.928 0.000 0.000 0.012 0.060
#> GSM152874 1 0.2597 0.76343 0.884 0.000 0.000 0.024 0.092
#> GSM152875 1 0.2171 0.76611 0.912 0.000 0.000 0.024 0.064
#> GSM152876 1 0.1907 0.74562 0.928 0.000 0.000 0.044 0.028
#> GSM152877 1 0.1557 0.77170 0.940 0.000 0.000 0.008 0.052
#> GSM152878 1 0.1668 0.76006 0.940 0.000 0.000 0.032 0.028
#> GSM152879 1 0.0955 0.76849 0.968 0.000 0.000 0.004 0.028
#> GSM152880 1 0.1270 0.76874 0.948 0.000 0.000 0.000 0.052
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.693 0.3868 0.016 0.536 0.052 0.104 0.264 0.028
#> GSM152805 5 0.161 0.7042 0.000 0.004 0.044 0.000 0.936 0.016
#> GSM152806 5 0.172 0.7134 0.000 0.000 0.032 0.000 0.928 0.040
#> GSM152807 2 0.221 0.7782 0.004 0.908 0.008 0.060 0.000 0.020
#> GSM152808 5 0.173 0.7104 0.000 0.000 0.012 0.012 0.932 0.044
#> GSM152809 2 0.161 0.7810 0.000 0.932 0.008 0.056 0.000 0.004
#> GSM152810 6 0.583 0.4200 0.016 0.000 0.016 0.160 0.196 0.612
#> GSM152811 5 0.333 0.6830 0.004 0.000 0.020 0.036 0.840 0.100
#> GSM152812 2 0.206 0.7779 0.000 0.924 0.012 0.024 0.028 0.012
#> GSM152813 2 0.296 0.7695 0.008 0.884 0.032 0.028 0.036 0.012
#> GSM152814 2 0.281 0.7668 0.008 0.888 0.016 0.016 0.056 0.016
#> GSM152815 2 0.203 0.7783 0.000 0.924 0.012 0.032 0.024 0.008
#> GSM152816 5 0.402 0.6779 0.008 0.036 0.076 0.044 0.820 0.016
#> GSM152817 5 0.169 0.7099 0.000 0.000 0.008 0.012 0.932 0.048
#> GSM152818 5 0.172 0.7109 0.000 0.000 0.036 0.004 0.932 0.028
#> GSM152819 5 0.335 0.6342 0.004 0.156 0.016 0.000 0.812 0.012
#> GSM152820 5 0.469 0.5913 0.000 0.068 0.016 0.156 0.740 0.020
#> GSM152821 2 0.331 0.7165 0.000 0.828 0.020 0.008 0.132 0.012
#> GSM153115 4 0.692 0.3285 0.092 0.088 0.316 0.480 0.000 0.024
#> GSM153116 5 0.453 0.6341 0.000 0.132 0.008 0.008 0.740 0.112
#> GSM153117 5 0.397 0.5610 0.000 0.252 0.012 0.004 0.720 0.012
#> GSM153118 2 0.275 0.7444 0.000 0.860 0.012 0.004 0.116 0.008
#> GSM153119 5 0.583 0.1321 0.004 0.024 0.064 0.008 0.456 0.444
#> GSM153120 6 0.609 0.3258 0.024 0.332 0.000 0.152 0.000 0.492
#> GSM153121 3 0.358 0.6773 0.000 0.004 0.804 0.000 0.120 0.072
#> GSM153122 6 0.596 0.3441 0.020 0.008 0.168 0.000 0.224 0.580
#> GSM153123 2 0.654 0.0113 0.000 0.420 0.404 0.028 0.020 0.128
#> GSM153124 3 0.633 0.0315 0.012 0.088 0.496 0.360 0.004 0.040
#> GSM153125 4 0.652 0.3666 0.024 0.304 0.128 0.512 0.000 0.032
#> GSM153126 3 0.276 0.6958 0.004 0.000 0.864 0.004 0.104 0.024
#> GSM153127 2 0.245 0.7756 0.000 0.900 0.016 0.032 0.004 0.048
#> GSM153128 6 0.488 0.5612 0.004 0.032 0.068 0.020 0.128 0.748
#> GSM153129 3 0.563 0.6043 0.000 0.072 0.664 0.068 0.184 0.012
#> GSM153130 5 0.498 0.0222 0.000 0.004 0.448 0.000 0.492 0.056
#> GSM153131 5 0.357 0.6694 0.008 0.036 0.128 0.000 0.816 0.012
#> GSM153132 5 0.454 0.6905 0.000 0.120 0.048 0.008 0.764 0.060
#> GSM153133 2 0.556 0.5037 0.000 0.636 0.188 0.036 0.000 0.140
#> GSM153134 5 0.645 0.0630 0.000 0.220 0.356 0.004 0.404 0.016
#> GSM153135 2 0.130 0.7816 0.000 0.952 0.004 0.032 0.000 0.012
#> GSM153136 4 0.765 0.3632 0.060 0.224 0.152 0.468 0.000 0.096
#> GSM153137 2 0.291 0.7540 0.000 0.852 0.000 0.072 0.000 0.076
#> GSM153138 2 0.476 0.6396 0.000 0.716 0.004 0.124 0.012 0.144
#> GSM153139 5 0.471 0.4984 0.000 0.036 0.272 0.004 0.668 0.020
#> GSM153140 2 0.652 0.3470 0.000 0.556 0.064 0.264 0.088 0.028
#> GSM153141 2 0.107 0.7806 0.000 0.960 0.000 0.028 0.000 0.012
#> GSM153142 5 0.331 0.7027 0.000 0.008 0.064 0.008 0.844 0.076
#> GSM153143 2 0.384 0.6743 0.000 0.788 0.008 0.084 0.000 0.120
#> GSM153144 2 0.297 0.7186 0.000 0.832 0.148 0.012 0.004 0.004
#> GSM153145 5 0.216 0.7129 0.000 0.000 0.028 0.008 0.908 0.056
#> GSM153146 2 0.220 0.7649 0.000 0.904 0.012 0.004 0.072 0.008
#> GSM153147 3 0.360 0.6894 0.000 0.044 0.828 0.000 0.072 0.056
#> GSM153148 2 0.104 0.7823 0.000 0.964 0.000 0.024 0.004 0.008
#> GSM153149 2 0.222 0.7667 0.000 0.904 0.020 0.000 0.064 0.012
#> GSM153150 6 0.642 0.1239 0.036 0.176 0.000 0.336 0.000 0.452
#> GSM153151 6 0.614 0.5087 0.000 0.196 0.184 0.012 0.028 0.580
#> GSM153152 2 0.661 0.2056 0.000 0.492 0.324 0.012 0.064 0.108
#> GSM153153 2 0.369 0.6680 0.000 0.780 0.020 0.008 0.184 0.008
#> GSM153154 5 0.534 0.5527 0.000 0.060 0.240 0.008 0.652 0.040
#> GSM153155 2 0.214 0.7829 0.000 0.908 0.016 0.064 0.012 0.000
#> GSM153156 3 0.463 0.5433 0.000 0.012 0.668 0.000 0.268 0.052
#> GSM153157 5 0.413 0.6634 0.000 0.000 0.040 0.052 0.780 0.128
#> GSM153158 5 0.330 0.7018 0.000 0.096 0.028 0.004 0.844 0.028
#> GSM153159 5 0.498 0.5755 0.000 0.008 0.200 0.004 0.676 0.112
#> GSM153160 3 0.319 0.6942 0.008 0.000 0.844 0.004 0.100 0.044
#> GSM153161 2 0.171 0.7757 0.000 0.928 0.000 0.028 0.000 0.044
#> GSM153162 3 0.265 0.7009 0.004 0.020 0.880 0.000 0.084 0.012
#> GSM153163 5 0.279 0.6646 0.004 0.000 0.144 0.000 0.840 0.012
#> GSM153164 5 0.428 0.5507 0.000 0.224 0.004 0.032 0.724 0.016
#> GSM153165 3 0.461 0.1540 0.000 0.016 0.516 0.004 0.456 0.008
#> GSM153166 5 0.514 0.0975 0.000 0.444 0.048 0.000 0.492 0.016
#> GSM153167 3 0.524 0.6298 0.000 0.124 0.700 0.040 0.128 0.008
#> GSM153168 5 0.345 0.6617 0.000 0.000 0.024 0.012 0.800 0.164
#> GSM153169 5 0.533 0.2581 0.000 0.000 0.356 0.000 0.528 0.116
#> GSM153170 3 0.438 0.5675 0.000 0.012 0.692 0.000 0.256 0.040
#> GSM153171 4 0.725 0.3124 0.128 0.024 0.304 0.448 0.000 0.096
#> GSM153172 2 0.122 0.7831 0.000 0.960 0.016 0.012 0.004 0.008
#> GSM153173 3 0.427 0.3552 0.000 0.000 0.596 0.000 0.380 0.024
#> GSM153174 3 0.278 0.6603 0.000 0.092 0.872 0.012 0.012 0.012
#> GSM153175 3 0.408 0.4948 0.020 0.008 0.744 0.212 0.000 0.016
#> GSM153176 3 0.416 0.6171 0.008 0.000 0.784 0.100 0.016 0.092
#> GSM153177 2 0.313 0.7092 0.000 0.824 0.016 0.000 0.148 0.012
#> GSM152931 4 0.745 0.3129 0.028 0.248 0.268 0.396 0.000 0.060
#> GSM152932 2 0.194 0.7760 0.000 0.924 0.036 0.000 0.024 0.016
#> GSM152933 2 0.448 0.1235 0.000 0.532 0.012 0.000 0.444 0.012
#> GSM152934 6 0.562 0.5671 0.000 0.084 0.096 0.108 0.020 0.692
#> GSM152935 6 0.653 0.5172 0.000 0.232 0.104 0.020 0.076 0.568
#> GSM152936 2 0.724 -0.2018 0.000 0.332 0.088 0.284 0.000 0.296
#> GSM152937 6 0.496 0.5083 0.004 0.016 0.200 0.008 0.072 0.700
#> GSM152938 3 0.490 0.5701 0.000 0.024 0.696 0.004 0.072 0.204
#> GSM152939 3 0.383 0.5823 0.028 0.024 0.808 0.124 0.000 0.016
#> GSM152940 6 0.538 0.2964 0.004 0.112 0.004 0.296 0.000 0.584
#> GSM152941 4 0.467 0.3874 0.088 0.012 0.004 0.716 0.000 0.180
#> GSM152942 3 0.253 0.7025 0.000 0.000 0.884 0.012 0.080 0.024
#> GSM152943 6 0.522 0.4824 0.004 0.216 0.020 0.100 0.000 0.660
#> GSM152944 5 0.397 0.6150 0.000 0.012 0.212 0.004 0.748 0.024
#> GSM152945 6 0.425 0.5818 0.004 0.128 0.032 0.028 0.020 0.788
#> GSM152946 2 0.662 0.4279 0.008 0.564 0.184 0.132 0.000 0.112
#> GSM152947 6 0.592 0.3337 0.052 0.004 0.096 0.256 0.000 0.592
#> GSM152948 2 0.171 0.7816 0.000 0.928 0.004 0.056 0.000 0.012
#> GSM152949 3 0.317 0.6949 0.000 0.024 0.844 0.000 0.104 0.028
#> GSM152950 3 0.777 0.0614 0.000 0.220 0.352 0.008 0.188 0.232
#> GSM152951 2 0.267 0.7695 0.000 0.880 0.016 0.072 0.000 0.032
#> GSM152952 2 0.179 0.7753 0.000 0.924 0.000 0.044 0.000 0.032
#> GSM152953 2 0.160 0.7854 0.000 0.944 0.004 0.020 0.012 0.020
#> GSM152954 4 0.359 0.4707 0.032 0.044 0.036 0.852 0.008 0.028
#> GSM152955 4 0.678 -0.1194 0.000 0.020 0.016 0.396 0.228 0.340
#> GSM152956 2 0.107 0.7813 0.000 0.960 0.000 0.028 0.000 0.012
#> GSM152957 3 0.579 0.0379 0.096 0.000 0.504 0.372 0.000 0.028
#> GSM152958 4 0.571 0.4394 0.080 0.212 0.028 0.648 0.000 0.032
#> GSM152959 4 0.394 0.4325 0.036 0.004 0.052 0.804 0.000 0.104
#> GSM152960 2 0.611 0.0594 0.004 0.436 0.000 0.300 0.000 0.260
#> GSM152961 4 0.519 0.4723 0.116 0.092 0.024 0.724 0.000 0.044
#> GSM152962 6 0.655 0.4056 0.000 0.116 0.236 0.004 0.100 0.544
#> GSM152963 2 0.148 0.7833 0.000 0.948 0.008 0.012 0.004 0.028
#> GSM152964 6 0.445 0.5516 0.012 0.008 0.020 0.048 0.144 0.768
#> GSM152965 2 0.496 0.3485 0.000 0.588 0.016 0.024 0.012 0.360
#> GSM152966 4 0.689 0.3741 0.032 0.260 0.200 0.480 0.000 0.028
#> GSM152967 2 0.330 0.7602 0.004 0.856 0.028 0.064 0.004 0.044
#> GSM152968 3 0.637 0.1971 0.000 0.148 0.472 0.000 0.336 0.044
#> GSM152969 4 0.476 0.4513 0.012 0.220 0.064 0.696 0.000 0.008
#> GSM152970 4 0.608 0.3652 0.112 0.008 0.072 0.616 0.000 0.192
#> GSM152971 4 0.706 0.2851 0.016 0.332 0.160 0.428 0.000 0.064
#> GSM152972 4 0.613 0.1187 0.008 0.412 0.028 0.448 0.000 0.104
#> GSM152973 3 0.230 0.6601 0.044 0.000 0.908 0.032 0.008 0.008
#> GSM152974 2 0.155 0.7803 0.000 0.940 0.036 0.000 0.004 0.020
#> GSM152975 2 0.663 0.4101 0.004 0.556 0.004 0.128 0.212 0.096
#> GSM152976 4 0.658 0.1617 0.128 0.000 0.388 0.416 0.000 0.068
#> GSM152977 4 0.472 0.3246 0.000 0.000 0.020 0.720 0.132 0.128
#> GSM152978 4 0.406 0.4209 0.000 0.204 0.012 0.748 0.004 0.032
#> GSM152979 3 0.455 0.5588 0.000 0.000 0.680 0.000 0.232 0.088
#> GSM152980 4 0.577 0.3550 0.000 0.228 0.016 0.628 0.092 0.036
#> GSM152981 5 0.578 0.1813 0.000 0.008 0.060 0.032 0.472 0.428
#> GSM152982 3 0.614 0.1732 0.004 0.020 0.516 0.320 0.004 0.136
#> GSM152983 4 0.605 0.3643 0.004 0.064 0.148 0.612 0.000 0.172
#> GSM152984 3 0.204 0.6791 0.004 0.000 0.920 0.040 0.028 0.008
#> GSM152985 4 0.478 0.2484 0.016 0.012 0.020 0.656 0.004 0.292
#> GSM152986 4 0.664 0.4413 0.072 0.184 0.092 0.596 0.000 0.056
#> GSM152987 6 0.456 0.3397 0.072 0.004 0.000 0.220 0.004 0.700
#> GSM152988 3 0.435 0.5730 0.096 0.008 0.776 0.100 0.004 0.016
#> GSM152989 4 0.480 0.4336 0.176 0.000 0.052 0.716 0.000 0.056
#> GSM152990 3 0.422 0.6476 0.000 0.008 0.752 0.000 0.148 0.092
#> GSM152991 5 0.655 0.2656 0.004 0.184 0.024 0.008 0.484 0.296
#> GSM187524 4 0.575 0.0775 0.104 0.000 0.000 0.492 0.020 0.384
#> GSM187525 4 0.560 0.2435 0.116 0.000 0.004 0.604 0.020 0.256
#> GSM187526 4 0.580 0.1736 0.272 0.000 0.004 0.552 0.008 0.164
#> GSM187527 1 0.248 0.8385 0.892 0.000 0.016 0.064 0.000 0.028
#> GSM152856 1 0.172 0.8456 0.940 0.008 0.016 0.016 0.000 0.020
#> GSM152857 1 0.167 0.8313 0.932 0.000 0.004 0.000 0.048 0.016
#> GSM152858 1 0.580 0.3455 0.484 0.000 0.008 0.380 0.004 0.124
#> GSM152859 6 0.635 -0.0294 0.164 0.000 0.004 0.372 0.024 0.436
#> GSM152860 4 0.649 0.0152 0.292 0.000 0.012 0.452 0.012 0.232
#> GSM152861 1 0.441 0.6542 0.676 0.000 0.000 0.260 0.000 0.064
#> GSM152862 4 0.633 -0.0388 0.324 0.000 0.008 0.460 0.012 0.196
#> GSM152863 1 0.280 0.8342 0.864 0.000 0.016 0.100 0.000 0.020
#> GSM152864 1 0.250 0.8267 0.868 0.000 0.004 0.116 0.000 0.012
#> GSM152865 1 0.353 0.7695 0.784 0.000 0.004 0.180 0.000 0.032
#> GSM152866 1 0.418 0.7163 0.740 0.000 0.004 0.076 0.000 0.180
#> GSM152867 1 0.216 0.8420 0.896 0.000 0.004 0.088 0.000 0.012
#> GSM152868 1 0.266 0.8272 0.860 0.000 0.008 0.120 0.000 0.012
#> GSM152869 1 0.266 0.8176 0.848 0.000 0.008 0.140 0.000 0.004
#> GSM152870 4 0.648 0.0596 0.280 0.000 0.008 0.472 0.020 0.220
#> GSM152871 1 0.510 0.4640 0.564 0.000 0.008 0.368 0.004 0.056
#> GSM152872 4 0.589 -0.2115 0.408 0.000 0.008 0.456 0.008 0.120
#> GSM152873 1 0.145 0.8485 0.948 0.000 0.012 0.020 0.000 0.020
#> GSM152874 1 0.209 0.8445 0.916 0.000 0.020 0.020 0.000 0.044
#> GSM152875 1 0.171 0.8466 0.936 0.000 0.016 0.020 0.000 0.028
#> GSM152876 1 0.186 0.8285 0.928 0.000 0.020 0.016 0.000 0.036
#> GSM152877 1 0.168 0.8490 0.940 0.004 0.012 0.020 0.000 0.024
#> GSM152878 1 0.145 0.8451 0.948 0.000 0.016 0.024 0.000 0.012
#> GSM152879 1 0.127 0.8489 0.956 0.000 0.012 0.020 0.000 0.012
#> GSM152880 1 0.185 0.8506 0.932 0.008 0.008 0.020 0.000 0.032
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> MAD:NMF 169 3.59e-14 2
#> MAD:NMF 137 1.39e-16 3
#> MAD:NMF 126 3.40e-20 4
#> MAD:NMF 104 1.48e-19 5
#> MAD:NMF 102 2.51e-20 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "hclust"]
# you can also extract it by
# res = res_list["ATC:hclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'hclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.499 0.839 0.920 0.3289 0.694 0.694
#> 3 3 0.496 0.653 0.833 0.3940 0.768 0.681
#> 4 4 0.483 0.689 0.836 0.0571 0.985 0.971
#> 5 5 0.466 0.717 0.842 0.1653 0.852 0.728
#> 6 6 0.464 0.616 0.787 0.0570 0.876 0.760
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.9147 0.000 1.000
#> GSM152805 2 0.0000 0.9147 0.000 1.000
#> GSM152806 2 0.0000 0.9147 0.000 1.000
#> GSM152807 2 0.0000 0.9147 0.000 1.000
#> GSM152808 2 0.0000 0.9147 0.000 1.000
#> GSM152809 2 0.0000 0.9147 0.000 1.000
#> GSM152810 1 0.9963 0.0839 0.536 0.464
#> GSM152811 2 0.0000 0.9147 0.000 1.000
#> GSM152812 2 0.0000 0.9147 0.000 1.000
#> GSM152813 2 0.0000 0.9147 0.000 1.000
#> GSM152814 2 0.0000 0.9147 0.000 1.000
#> GSM152815 2 0.0000 0.9147 0.000 1.000
#> GSM152816 2 0.0000 0.9147 0.000 1.000
#> GSM152817 2 0.0000 0.9147 0.000 1.000
#> GSM152818 2 0.0000 0.9147 0.000 1.000
#> GSM152819 2 0.0000 0.9147 0.000 1.000
#> GSM152820 2 0.0000 0.9147 0.000 1.000
#> GSM152821 2 0.0000 0.9147 0.000 1.000
#> GSM153115 2 0.6048 0.7995 0.148 0.852
#> GSM153116 2 0.0000 0.9147 0.000 1.000
#> GSM153117 2 0.0000 0.9147 0.000 1.000
#> GSM153118 2 0.0000 0.9147 0.000 1.000
#> GSM153119 2 0.0000 0.9147 0.000 1.000
#> GSM153120 2 0.9635 0.3936 0.388 0.612
#> GSM153121 2 0.0000 0.9147 0.000 1.000
#> GSM153122 2 0.0000 0.9147 0.000 1.000
#> GSM153123 2 0.0000 0.9147 0.000 1.000
#> GSM153124 2 0.6247 0.7917 0.156 0.844
#> GSM153125 2 0.6247 0.7917 0.156 0.844
#> GSM153126 2 0.0000 0.9147 0.000 1.000
#> GSM153127 2 0.0000 0.9147 0.000 1.000
#> GSM153128 2 0.0938 0.9073 0.012 0.988
#> GSM153129 2 0.0000 0.9147 0.000 1.000
#> GSM153130 2 0.0000 0.9147 0.000 1.000
#> GSM153131 2 0.0000 0.9147 0.000 1.000
#> GSM153132 2 0.0000 0.9147 0.000 1.000
#> GSM153133 2 0.0000 0.9147 0.000 1.000
#> GSM153134 2 0.0000 0.9147 0.000 1.000
#> GSM153135 2 0.0000 0.9147 0.000 1.000
#> GSM153136 2 0.8661 0.6142 0.288 0.712
#> GSM153137 2 0.7950 0.6880 0.240 0.760
#> GSM153138 2 0.7602 0.7148 0.220 0.780
#> GSM153139 2 0.0000 0.9147 0.000 1.000
#> GSM153140 2 0.0000 0.9147 0.000 1.000
#> GSM153141 2 0.0000 0.9147 0.000 1.000
#> GSM153142 2 0.0000 0.9147 0.000 1.000
#> GSM153143 2 0.0000 0.9147 0.000 1.000
#> GSM153144 2 0.0000 0.9147 0.000 1.000
#> GSM153145 2 0.0000 0.9147 0.000 1.000
#> GSM153146 2 0.0000 0.9147 0.000 1.000
#> GSM153147 2 0.0000 0.9147 0.000 1.000
#> GSM153148 2 0.0000 0.9147 0.000 1.000
#> GSM153149 2 0.0000 0.9147 0.000 1.000
#> GSM153150 2 0.8861 0.5842 0.304 0.696
#> GSM153151 2 0.0000 0.9147 0.000 1.000
#> GSM153152 2 0.0000 0.9147 0.000 1.000
#> GSM153153 2 0.0000 0.9147 0.000 1.000
#> GSM153154 2 0.0000 0.9147 0.000 1.000
#> GSM153155 2 0.0376 0.9123 0.004 0.996
#> GSM153156 2 0.0000 0.9147 0.000 1.000
#> GSM153157 2 0.0000 0.9147 0.000 1.000
#> GSM153158 2 0.0000 0.9147 0.000 1.000
#> GSM153159 2 0.0000 0.9147 0.000 1.000
#> GSM153160 2 0.0000 0.9147 0.000 1.000
#> GSM153161 2 0.0000 0.9147 0.000 1.000
#> GSM153162 2 0.0000 0.9147 0.000 1.000
#> GSM153163 2 0.0000 0.9147 0.000 1.000
#> GSM153164 2 0.0000 0.9147 0.000 1.000
#> GSM153165 2 0.0000 0.9147 0.000 1.000
#> GSM153166 2 0.0000 0.9147 0.000 1.000
#> GSM153167 2 0.0000 0.9147 0.000 1.000
#> GSM153168 2 0.0000 0.9147 0.000 1.000
#> GSM153169 2 0.0000 0.9147 0.000 1.000
#> GSM153170 2 0.0000 0.9147 0.000 1.000
#> GSM153171 2 0.6048 0.7995 0.148 0.852
#> GSM153172 2 0.0000 0.9147 0.000 1.000
#> GSM153173 2 0.0000 0.9147 0.000 1.000
#> GSM153174 2 0.0000 0.9147 0.000 1.000
#> GSM153175 2 0.6438 0.7833 0.164 0.836
#> GSM153176 2 0.0000 0.9147 0.000 1.000
#> GSM153177 2 0.0000 0.9147 0.000 1.000
#> GSM152931 2 0.8081 0.6763 0.248 0.752
#> GSM152932 2 0.0000 0.9147 0.000 1.000
#> GSM152933 2 0.0000 0.9147 0.000 1.000
#> GSM152934 2 0.5629 0.8146 0.132 0.868
#> GSM152935 2 0.0000 0.9147 0.000 1.000
#> GSM152936 2 0.8861 0.5842 0.304 0.696
#> GSM152937 2 0.0938 0.9073 0.012 0.988
#> GSM152938 2 0.0000 0.9147 0.000 1.000
#> GSM152939 2 0.7528 0.7208 0.216 0.784
#> GSM152940 2 0.9635 0.3936 0.388 0.612
#> GSM152941 1 0.7056 0.8387 0.808 0.192
#> GSM152942 2 0.0000 0.9147 0.000 1.000
#> GSM152943 2 0.5629 0.8146 0.132 0.868
#> GSM152944 2 0.0000 0.9147 0.000 1.000
#> GSM152945 2 0.0000 0.9147 0.000 1.000
#> GSM152946 2 0.0000 0.9147 0.000 1.000
#> GSM152947 2 0.8386 0.6475 0.268 0.732
#> GSM152948 2 0.0000 0.9147 0.000 1.000
#> GSM152949 2 0.0000 0.9147 0.000 1.000
#> GSM152950 2 0.0000 0.9147 0.000 1.000
#> GSM152951 2 0.0376 0.9123 0.004 0.996
#> GSM152952 2 0.0000 0.9147 0.000 1.000
#> GSM152953 2 0.0000 0.9147 0.000 1.000
#> GSM152954 2 0.8861 0.5842 0.304 0.696
#> GSM152955 2 0.1633 0.8998 0.024 0.976
#> GSM152956 2 0.0000 0.9147 0.000 1.000
#> GSM152957 2 0.9170 0.5283 0.332 0.668
#> GSM152958 2 0.9286 0.5018 0.344 0.656
#> GSM152959 2 0.9460 0.4543 0.364 0.636
#> GSM152960 2 0.8909 0.5771 0.308 0.692
#> GSM152961 2 0.9635 0.3936 0.388 0.612
#> GSM152962 2 0.0000 0.9147 0.000 1.000
#> GSM152963 2 0.0000 0.9147 0.000 1.000
#> GSM152964 2 0.0938 0.9073 0.012 0.988
#> GSM152965 2 0.0000 0.9147 0.000 1.000
#> GSM152966 2 0.8713 0.6067 0.292 0.708
#> GSM152967 2 0.0376 0.9124 0.004 0.996
#> GSM152968 2 0.0000 0.9147 0.000 1.000
#> GSM152969 2 0.8713 0.6067 0.292 0.708
#> GSM152970 2 0.9608 0.4045 0.384 0.616
#> GSM152971 2 0.8661 0.6136 0.288 0.712
#> GSM152972 2 0.8763 0.5996 0.296 0.704
#> GSM152973 2 0.0000 0.9147 0.000 1.000
#> GSM152974 2 0.0000 0.9147 0.000 1.000
#> GSM152975 2 0.5629 0.8148 0.132 0.868
#> GSM152976 2 0.3431 0.8715 0.064 0.936
#> GSM152977 2 0.7453 0.7278 0.212 0.788
#> GSM152978 2 0.9635 0.3936 0.388 0.612
#> GSM152979 2 0.0000 0.9147 0.000 1.000
#> GSM152980 2 0.0376 0.9123 0.004 0.996
#> GSM152981 2 0.0000 0.9147 0.000 1.000
#> GSM152982 2 0.6048 0.8004 0.148 0.852
#> GSM152983 2 0.6048 0.8004 0.148 0.852
#> GSM152984 2 0.0000 0.9147 0.000 1.000
#> GSM152985 2 0.9635 0.3936 0.388 0.612
#> GSM152986 2 0.8909 0.5776 0.308 0.692
#> GSM152987 1 0.5737 0.9055 0.864 0.136
#> GSM152988 2 0.6801 0.7651 0.180 0.820
#> GSM152989 2 0.9460 0.4543 0.364 0.636
#> GSM152990 2 0.0000 0.9147 0.000 1.000
#> GSM152991 2 0.0000 0.9147 0.000 1.000
#> GSM187524 1 0.0000 0.8571 1.000 0.000
#> GSM187525 1 0.0000 0.8571 1.000 0.000
#> GSM187526 1 0.0000 0.8571 1.000 0.000
#> GSM187527 1 0.8763 0.6647 0.704 0.296
#> GSM152856 1 0.5737 0.9055 0.864 0.136
#> GSM152857 1 0.8763 0.6712 0.704 0.296
#> GSM152858 1 0.0000 0.8571 1.000 0.000
#> GSM152859 1 0.0000 0.8571 1.000 0.000
#> GSM152860 1 0.0000 0.8571 1.000 0.000
#> GSM152861 1 0.5737 0.9055 0.864 0.136
#> GSM152862 1 0.0000 0.8571 1.000 0.000
#> GSM152863 1 0.5842 0.9021 0.860 0.140
#> GSM152864 1 0.5737 0.9055 0.864 0.136
#> GSM152865 1 0.5737 0.9055 0.864 0.136
#> GSM152866 1 0.5737 0.9055 0.864 0.136
#> GSM152867 1 0.5737 0.9055 0.864 0.136
#> GSM152868 1 0.5737 0.9055 0.864 0.136
#> GSM152869 1 0.5737 0.9055 0.864 0.136
#> GSM152870 1 0.0000 0.8571 1.000 0.000
#> GSM152871 1 0.0000 0.8571 1.000 0.000
#> GSM152872 1 0.0000 0.8571 1.000 0.000
#> GSM152873 1 0.5737 0.9055 0.864 0.136
#> GSM152874 1 0.5737 0.9055 0.864 0.136
#> GSM152875 1 0.5842 0.9021 0.860 0.140
#> GSM152876 1 0.6343 0.8807 0.840 0.160
#> GSM152877 1 0.5737 0.9055 0.864 0.136
#> GSM152878 1 0.5737 0.9055 0.864 0.136
#> GSM152879 1 0.5737 0.9055 0.864 0.136
#> GSM152880 1 0.5737 0.9055 0.864 0.136
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 3 0.3038 0.86946 0.000 0.104 0.896
#> GSM152805 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM152806 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM152807 3 0.3038 0.86946 0.000 0.104 0.896
#> GSM152808 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM152809 3 0.3038 0.86946 0.000 0.104 0.896
#> GSM152810 1 0.9676 0.26839 0.432 0.348 0.220
#> GSM152811 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM152812 3 0.3038 0.86946 0.000 0.104 0.896
#> GSM152813 3 0.3038 0.86946 0.000 0.104 0.896
#> GSM152814 3 0.3038 0.86946 0.000 0.104 0.896
#> GSM152815 3 0.3038 0.86946 0.000 0.104 0.896
#> GSM152816 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM152817 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM152818 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM152819 3 0.0237 0.88238 0.000 0.004 0.996
#> GSM152820 3 0.1860 0.88671 0.000 0.052 0.948
#> GSM152821 3 0.2625 0.87995 0.000 0.084 0.916
#> GSM153115 3 0.6079 0.38937 0.000 0.388 0.612
#> GSM153116 3 0.0000 0.88350 0.000 0.000 1.000
#> GSM153117 3 0.0000 0.88350 0.000 0.000 1.000
#> GSM153118 3 0.1964 0.88566 0.000 0.056 0.944
#> GSM153119 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM153120 2 0.5327 0.54632 0.000 0.728 0.272
#> GSM153121 3 0.0592 0.88257 0.000 0.012 0.988
#> GSM153122 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM153123 3 0.2625 0.87886 0.000 0.084 0.916
#> GSM153124 3 0.6126 0.35989 0.000 0.400 0.600
#> GSM153125 3 0.6140 0.34861 0.000 0.404 0.596
#> GSM153126 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM153127 3 0.3116 0.86742 0.000 0.108 0.892
#> GSM153128 3 0.3030 0.83547 0.004 0.092 0.904
#> GSM153129 3 0.0000 0.88350 0.000 0.000 1.000
#> GSM153130 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM153131 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM153132 3 0.0000 0.88350 0.000 0.000 1.000
#> GSM153133 3 0.2711 0.87847 0.000 0.088 0.912
#> GSM153134 3 0.1753 0.88617 0.000 0.048 0.952
#> GSM153135 3 0.3116 0.86742 0.000 0.108 0.892
#> GSM153136 2 0.6111 0.40789 0.000 0.604 0.396
#> GSM153137 2 0.6309 0.05498 0.000 0.500 0.500
#> GSM153138 3 0.6299 0.02708 0.000 0.476 0.524
#> GSM153139 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM153140 3 0.3038 0.86946 0.000 0.104 0.896
#> GSM153141 3 0.3116 0.86742 0.000 0.108 0.892
#> GSM153142 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM153143 3 0.3038 0.87219 0.000 0.104 0.896
#> GSM153144 3 0.1163 0.88681 0.000 0.028 0.972
#> GSM153145 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM153146 3 0.2537 0.88115 0.000 0.080 0.920
#> GSM153147 3 0.2537 0.88122 0.000 0.080 0.920
#> GSM153148 3 0.3116 0.86742 0.000 0.108 0.892
#> GSM153149 3 0.2625 0.87993 0.000 0.084 0.916
#> GSM153150 2 0.6045 0.44078 0.000 0.620 0.380
#> GSM153151 3 0.2711 0.87847 0.000 0.088 0.912
#> GSM153152 3 0.0892 0.88628 0.000 0.020 0.980
#> GSM153153 3 0.2066 0.88533 0.000 0.060 0.940
#> GSM153154 3 0.0000 0.88350 0.000 0.000 1.000
#> GSM153155 3 0.3116 0.87096 0.000 0.108 0.892
#> GSM153156 3 0.0592 0.88257 0.000 0.012 0.988
#> GSM153157 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM153158 3 0.0000 0.88350 0.000 0.000 1.000
#> GSM153159 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM153160 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM153161 3 0.3116 0.86742 0.000 0.108 0.892
#> GSM153162 3 0.1163 0.88681 0.000 0.028 0.972
#> GSM153163 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM153164 3 0.0000 0.88350 0.000 0.000 1.000
#> GSM153165 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM153166 3 0.1753 0.88617 0.000 0.048 0.952
#> GSM153167 3 0.0000 0.88350 0.000 0.000 1.000
#> GSM153168 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM153169 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM153170 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM153171 3 0.6079 0.38937 0.000 0.388 0.612
#> GSM153172 3 0.2356 0.88240 0.000 0.072 0.928
#> GSM153173 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM153174 3 0.1163 0.88681 0.000 0.028 0.972
#> GSM153175 3 0.6180 0.31083 0.000 0.416 0.584
#> GSM153176 3 0.3482 0.84883 0.000 0.128 0.872
#> GSM153177 3 0.1753 0.88617 0.000 0.048 0.952
#> GSM152931 2 0.6252 0.26401 0.000 0.556 0.444
#> GSM152932 3 0.2261 0.88312 0.000 0.068 0.932
#> GSM152933 3 0.1964 0.88566 0.000 0.056 0.944
#> GSM152934 3 0.6026 0.42111 0.000 0.376 0.624
#> GSM152935 3 0.1643 0.88665 0.000 0.044 0.956
#> GSM152936 2 0.6045 0.44078 0.000 0.620 0.380
#> GSM152937 3 0.3030 0.83547 0.004 0.092 0.904
#> GSM152938 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM152939 3 0.6309 -0.07589 0.000 0.500 0.500
#> GSM152940 2 0.5327 0.54632 0.000 0.728 0.272
#> GSM152941 2 0.7130 0.00758 0.432 0.544 0.024
#> GSM152942 3 0.0000 0.88350 0.000 0.000 1.000
#> GSM152943 3 0.6026 0.42111 0.000 0.376 0.624
#> GSM152944 3 0.0000 0.88350 0.000 0.000 1.000
#> GSM152945 3 0.2959 0.87146 0.000 0.100 0.900
#> GSM152946 3 0.3038 0.86946 0.000 0.104 0.896
#> GSM152947 2 0.6180 0.35199 0.000 0.584 0.416
#> GSM152948 3 0.3038 0.86946 0.000 0.104 0.896
#> GSM152949 3 0.0424 0.88395 0.000 0.008 0.992
#> GSM152950 3 0.1163 0.88643 0.000 0.028 0.972
#> GSM152951 3 0.3116 0.86781 0.000 0.108 0.892
#> GSM152952 3 0.3116 0.86742 0.000 0.108 0.892
#> GSM152953 3 0.3116 0.86742 0.000 0.108 0.892
#> GSM152954 2 0.6045 0.44078 0.000 0.620 0.380
#> GSM152955 3 0.4062 0.81584 0.000 0.164 0.836
#> GSM152956 3 0.3116 0.86742 0.000 0.108 0.892
#> GSM152957 2 0.5926 0.48417 0.000 0.644 0.356
#> GSM152958 2 0.5706 0.52956 0.000 0.680 0.320
#> GSM152959 2 0.5650 0.54276 0.000 0.688 0.312
#> GSM152960 2 0.6140 0.39773 0.000 0.596 0.404
#> GSM152961 2 0.5327 0.54632 0.000 0.728 0.272
#> GSM152962 3 0.2625 0.87993 0.000 0.084 0.916
#> GSM152963 3 0.3116 0.86742 0.000 0.108 0.892
#> GSM152964 3 0.3030 0.83547 0.004 0.092 0.904
#> GSM152965 3 0.2711 0.87847 0.000 0.088 0.912
#> GSM152966 2 0.6079 0.42633 0.000 0.612 0.388
#> GSM152967 3 0.2625 0.88014 0.000 0.084 0.916
#> GSM152968 3 0.0000 0.88350 0.000 0.000 1.000
#> GSM152969 2 0.6079 0.42633 0.000 0.612 0.388
#> GSM152970 2 0.5363 0.54744 0.000 0.724 0.276
#> GSM152971 2 0.6095 0.41678 0.000 0.608 0.392
#> GSM152972 2 0.6062 0.43478 0.000 0.616 0.384
#> GSM152973 3 0.2878 0.87047 0.000 0.096 0.904
#> GSM152974 3 0.1964 0.88521 0.000 0.056 0.944
#> GSM152975 3 0.5560 0.57849 0.000 0.300 0.700
#> GSM152976 3 0.5327 0.65300 0.000 0.272 0.728
#> GSM152977 3 0.6286 0.12670 0.000 0.464 0.536
#> GSM152978 2 0.5327 0.54632 0.000 0.728 0.272
#> GSM152979 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM152980 3 0.3267 0.86617 0.000 0.116 0.884
#> GSM152981 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM152982 3 0.6079 0.39599 0.000 0.388 0.612
#> GSM152983 3 0.6079 0.39599 0.000 0.388 0.612
#> GSM152984 3 0.2878 0.86928 0.000 0.096 0.904
#> GSM152985 2 0.5327 0.54632 0.000 0.728 0.272
#> GSM152986 2 0.5988 0.46240 0.000 0.632 0.368
#> GSM152987 2 0.6305 -0.09093 0.484 0.516 0.000
#> GSM152988 3 0.6252 0.15332 0.000 0.444 0.556
#> GSM152989 2 0.5650 0.54276 0.000 0.688 0.312
#> GSM152990 3 0.0424 0.88091 0.000 0.008 0.992
#> GSM152991 3 0.0747 0.87740 0.000 0.016 0.984
#> GSM187524 1 0.2711 0.85932 0.912 0.088 0.000
#> GSM187525 1 0.2796 0.86241 0.908 0.092 0.000
#> GSM187526 1 0.2796 0.86241 0.908 0.092 0.000
#> GSM187527 2 0.6512 0.15765 0.300 0.676 0.024
#> GSM152856 2 0.6291 -0.05789 0.468 0.532 0.000
#> GSM152857 2 0.7992 0.13857 0.328 0.592 0.080
#> GSM152858 1 0.2796 0.86241 0.908 0.092 0.000
#> GSM152859 1 0.2959 0.72021 0.900 0.100 0.000
#> GSM152860 1 0.2796 0.86241 0.908 0.092 0.000
#> GSM152861 2 0.6309 -0.10743 0.496 0.504 0.000
#> GSM152862 1 0.2796 0.86241 0.908 0.092 0.000
#> GSM152863 2 0.6295 -0.06965 0.472 0.528 0.000
#> GSM152864 2 0.6309 -0.10743 0.496 0.504 0.000
#> GSM152865 2 0.6309 -0.10743 0.496 0.504 0.000
#> GSM152866 1 0.6295 0.08745 0.528 0.472 0.000
#> GSM152867 2 0.6309 -0.10743 0.496 0.504 0.000
#> GSM152868 2 0.6309 -0.10743 0.496 0.504 0.000
#> GSM152869 2 0.6309 -0.10743 0.496 0.504 0.000
#> GSM152870 1 0.2796 0.86241 0.908 0.092 0.000
#> GSM152871 1 0.2796 0.86241 0.908 0.092 0.000
#> GSM152872 1 0.2796 0.86241 0.908 0.092 0.000
#> GSM152873 2 0.6291 -0.05789 0.468 0.532 0.000
#> GSM152874 2 0.6291 -0.05789 0.468 0.532 0.000
#> GSM152875 2 0.6267 -0.04210 0.452 0.548 0.000
#> GSM152876 2 0.6442 -0.01378 0.432 0.564 0.004
#> GSM152877 2 0.6291 -0.05789 0.468 0.532 0.000
#> GSM152878 2 0.6291 -0.05789 0.468 0.532 0.000
#> GSM152879 2 0.6291 -0.05789 0.468 0.532 0.000
#> GSM152880 2 0.6291 -0.05789 0.468 0.532 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.2760 0.8410 0.000 0.872 0.000 0.128
#> GSM152805 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM152806 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM152807 2 0.2704 0.8428 0.000 0.876 0.000 0.124
#> GSM152808 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM152809 2 0.2704 0.8428 0.000 0.876 0.000 0.124
#> GSM152810 3 0.4026 0.0000 0.012 0.092 0.848 0.048
#> GSM152811 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM152812 2 0.2704 0.8428 0.000 0.876 0.000 0.124
#> GSM152813 2 0.2704 0.8428 0.000 0.876 0.000 0.124
#> GSM152814 2 0.2704 0.8428 0.000 0.876 0.000 0.124
#> GSM152815 2 0.2704 0.8428 0.000 0.876 0.000 0.124
#> GSM152816 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM152817 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM152818 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM152819 2 0.0707 0.8611 0.000 0.980 0.020 0.000
#> GSM152820 2 0.1888 0.8678 0.000 0.940 0.016 0.044
#> GSM152821 2 0.2401 0.8579 0.000 0.904 0.004 0.092
#> GSM153115 2 0.5050 0.3317 0.000 0.588 0.004 0.408
#> GSM153116 2 0.0592 0.8621 0.000 0.984 0.016 0.000
#> GSM153117 2 0.0927 0.8644 0.000 0.976 0.016 0.008
#> GSM153118 2 0.1637 0.8658 0.000 0.940 0.000 0.060
#> GSM153119 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM153120 4 0.4188 0.5490 0.000 0.244 0.004 0.752
#> GSM153121 2 0.1209 0.8587 0.000 0.964 0.032 0.004
#> GSM153122 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM153123 2 0.2216 0.8577 0.000 0.908 0.000 0.092
#> GSM153124 2 0.4916 0.3018 0.000 0.576 0.000 0.424
#> GSM153125 2 0.4925 0.2896 0.000 0.572 0.000 0.428
#> GSM153126 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM153127 2 0.2760 0.8406 0.000 0.872 0.000 0.128
#> GSM153128 2 0.3749 0.7679 0.000 0.840 0.128 0.032
#> GSM153129 2 0.0336 0.8639 0.000 0.992 0.008 0.000
#> GSM153130 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM153131 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM153132 2 0.0592 0.8621 0.000 0.984 0.016 0.000
#> GSM153133 2 0.2593 0.8532 0.000 0.892 0.004 0.104
#> GSM153134 2 0.1474 0.8661 0.000 0.948 0.000 0.052
#> GSM153135 2 0.2704 0.8433 0.000 0.876 0.000 0.124
#> GSM153136 4 0.4746 0.4559 0.000 0.368 0.000 0.632
#> GSM153137 4 0.4989 0.1350 0.000 0.472 0.000 0.528
#> GSM153138 2 0.5000 -0.0446 0.000 0.500 0.000 0.500
#> GSM153139 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM153140 2 0.2760 0.8410 0.000 0.872 0.000 0.128
#> GSM153141 2 0.2760 0.8406 0.000 0.872 0.000 0.128
#> GSM153142 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM153143 2 0.2831 0.8460 0.000 0.876 0.004 0.120
#> GSM153144 2 0.0707 0.8673 0.000 0.980 0.000 0.020
#> GSM153145 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM153146 2 0.2401 0.8580 0.000 0.904 0.004 0.092
#> GSM153147 2 0.2266 0.8603 0.000 0.912 0.004 0.084
#> GSM153148 2 0.2760 0.8406 0.000 0.872 0.000 0.128
#> GSM153149 2 0.2466 0.8564 0.000 0.900 0.004 0.096
#> GSM153150 4 0.4679 0.4823 0.000 0.352 0.000 0.648
#> GSM153151 2 0.2593 0.8532 0.000 0.892 0.004 0.104
#> GSM153152 2 0.1174 0.8667 0.000 0.968 0.012 0.020
#> GSM153153 2 0.1716 0.8656 0.000 0.936 0.000 0.064
#> GSM153154 2 0.0469 0.8631 0.000 0.988 0.012 0.000
#> GSM153155 2 0.2888 0.8443 0.000 0.872 0.004 0.124
#> GSM153156 2 0.1209 0.8587 0.000 0.964 0.032 0.004
#> GSM153157 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM153158 2 0.0592 0.8621 0.000 0.984 0.016 0.000
#> GSM153159 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM153160 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM153161 2 0.2760 0.8406 0.000 0.872 0.000 0.128
#> GSM153162 2 0.0707 0.8673 0.000 0.980 0.000 0.020
#> GSM153163 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM153164 2 0.0927 0.8644 0.000 0.976 0.016 0.008
#> GSM153165 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM153166 2 0.1474 0.8661 0.000 0.948 0.000 0.052
#> GSM153167 2 0.0524 0.8648 0.000 0.988 0.008 0.004
#> GSM153168 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM153169 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM153170 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM153171 2 0.5050 0.3317 0.000 0.588 0.004 0.408
#> GSM153172 2 0.1867 0.8634 0.000 0.928 0.000 0.072
#> GSM153173 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM153174 2 0.0707 0.8673 0.000 0.980 0.000 0.020
#> GSM153175 2 0.4948 0.2483 0.000 0.560 0.000 0.440
#> GSM153176 2 0.3377 0.8255 0.000 0.848 0.012 0.140
#> GSM153177 2 0.1474 0.8661 0.000 0.948 0.000 0.052
#> GSM152931 4 0.4898 0.3297 0.000 0.416 0.000 0.584
#> GSM152932 2 0.1867 0.8629 0.000 0.928 0.000 0.072
#> GSM152933 2 0.1637 0.8658 0.000 0.940 0.000 0.060
#> GSM152934 2 0.5016 0.3706 0.000 0.600 0.004 0.396
#> GSM152935 2 0.1302 0.8669 0.000 0.956 0.000 0.044
#> GSM152936 4 0.4679 0.4823 0.000 0.352 0.000 0.648
#> GSM152937 2 0.3749 0.7679 0.000 0.840 0.128 0.032
#> GSM152938 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM152939 4 0.4989 0.1390 0.000 0.472 0.000 0.528
#> GSM152940 4 0.4188 0.5490 0.000 0.244 0.004 0.752
#> GSM152941 4 0.5663 0.3455 0.208 0.012 0.060 0.720
#> GSM152942 2 0.0336 0.8639 0.000 0.992 0.008 0.000
#> GSM152943 2 0.5016 0.3706 0.000 0.600 0.004 0.396
#> GSM152944 2 0.0817 0.8599 0.000 0.976 0.024 0.000
#> GSM152945 2 0.2647 0.8450 0.000 0.880 0.000 0.120
#> GSM152946 2 0.2760 0.8410 0.000 0.872 0.000 0.128
#> GSM152947 4 0.4991 0.4068 0.000 0.388 0.004 0.608
#> GSM152948 2 0.2760 0.8410 0.000 0.872 0.000 0.128
#> GSM152949 2 0.0657 0.8646 0.000 0.984 0.012 0.004
#> GSM152950 2 0.1284 0.8673 0.000 0.964 0.012 0.024
#> GSM152951 2 0.2814 0.8388 0.000 0.868 0.000 0.132
#> GSM152952 2 0.2760 0.8406 0.000 0.872 0.000 0.128
#> GSM152953 2 0.2760 0.8406 0.000 0.872 0.000 0.128
#> GSM152954 4 0.4679 0.4823 0.000 0.352 0.000 0.648
#> GSM152955 2 0.3539 0.7915 0.000 0.820 0.004 0.176
#> GSM152956 2 0.2760 0.8406 0.000 0.872 0.000 0.128
#> GSM152957 4 0.4564 0.5217 0.000 0.328 0.000 0.672
#> GSM152958 4 0.4535 0.5448 0.000 0.292 0.004 0.704
#> GSM152959 4 0.4483 0.5452 0.000 0.284 0.004 0.712
#> GSM152960 4 0.4776 0.4440 0.000 0.376 0.000 0.624
#> GSM152961 4 0.4188 0.5490 0.000 0.244 0.004 0.752
#> GSM152962 2 0.2401 0.8579 0.000 0.904 0.004 0.092
#> GSM152963 2 0.2760 0.8406 0.000 0.872 0.000 0.128
#> GSM152964 2 0.3749 0.7679 0.000 0.840 0.128 0.032
#> GSM152965 2 0.2530 0.8548 0.000 0.896 0.004 0.100
#> GSM152966 4 0.4713 0.4723 0.000 0.360 0.000 0.640
#> GSM152967 2 0.2281 0.8574 0.000 0.904 0.000 0.096
#> GSM152968 2 0.0469 0.8631 0.000 0.988 0.012 0.000
#> GSM152969 4 0.4713 0.4723 0.000 0.360 0.000 0.640
#> GSM152970 4 0.4220 0.5494 0.000 0.248 0.004 0.748
#> GSM152971 4 0.4730 0.4637 0.000 0.364 0.000 0.636
#> GSM152972 4 0.4697 0.4798 0.000 0.356 0.000 0.644
#> GSM152973 2 0.2714 0.8478 0.000 0.884 0.004 0.112
#> GSM152974 2 0.1637 0.8650 0.000 0.940 0.000 0.060
#> GSM152975 2 0.4543 0.5364 0.000 0.676 0.000 0.324
#> GSM152976 2 0.4406 0.6080 0.000 0.700 0.000 0.300
#> GSM152977 2 0.4999 0.0438 0.000 0.508 0.000 0.492
#> GSM152978 4 0.4188 0.5490 0.000 0.244 0.004 0.752
#> GSM152979 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM152980 2 0.2999 0.8394 0.000 0.864 0.004 0.132
#> GSM152981 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM152982 2 0.4898 0.3304 0.000 0.584 0.000 0.416
#> GSM152983 2 0.4898 0.3304 0.000 0.584 0.000 0.416
#> GSM152984 2 0.2714 0.8467 0.000 0.884 0.004 0.112
#> GSM152985 4 0.4188 0.5490 0.000 0.244 0.004 0.752
#> GSM152986 4 0.4800 0.5046 0.000 0.340 0.004 0.656
#> GSM152987 4 0.5496 0.3549 0.160 0.000 0.108 0.732
#> GSM152988 2 0.4985 0.0769 0.000 0.532 0.000 0.468
#> GSM152989 4 0.4483 0.5452 0.000 0.284 0.004 0.712
#> GSM152990 2 0.1022 0.8570 0.000 0.968 0.032 0.000
#> GSM152991 2 0.1211 0.8533 0.000 0.960 0.040 0.000
#> GSM187524 1 0.1059 0.9186 0.972 0.000 0.016 0.012
#> GSM187525 1 0.1182 0.9235 0.968 0.000 0.016 0.016
#> GSM187526 1 0.1182 0.9235 0.968 0.000 0.016 0.016
#> GSM187527 4 0.3867 0.4007 0.044 0.024 0.068 0.864
#> GSM152856 4 0.5332 0.3741 0.128 0.000 0.124 0.748
#> GSM152857 4 0.5013 0.3945 0.044 0.076 0.072 0.808
#> GSM152858 1 0.1118 0.9413 0.964 0.000 0.000 0.036
#> GSM152859 1 0.4543 0.5216 0.676 0.000 0.324 0.000
#> GSM152860 1 0.1118 0.9413 0.964 0.000 0.000 0.036
#> GSM152861 4 0.5624 0.3469 0.172 0.000 0.108 0.720
#> GSM152862 1 0.1118 0.9413 0.964 0.000 0.000 0.036
#> GSM152863 4 0.5361 0.3653 0.148 0.000 0.108 0.744
#> GSM152864 4 0.5624 0.3469 0.172 0.000 0.108 0.720
#> GSM152865 4 0.5624 0.3469 0.172 0.000 0.108 0.720
#> GSM152866 4 0.5772 0.2384 0.260 0.000 0.068 0.672
#> GSM152867 4 0.5624 0.3469 0.172 0.000 0.108 0.720
#> GSM152868 4 0.5624 0.3469 0.172 0.000 0.108 0.720
#> GSM152869 4 0.5624 0.3469 0.172 0.000 0.108 0.720
#> GSM152870 1 0.1118 0.9413 0.964 0.000 0.000 0.036
#> GSM152871 1 0.1118 0.9413 0.964 0.000 0.000 0.036
#> GSM152872 1 0.1118 0.9413 0.964 0.000 0.000 0.036
#> GSM152873 4 0.5332 0.3741 0.128 0.000 0.124 0.748
#> GSM152874 4 0.5332 0.3741 0.128 0.000 0.124 0.748
#> GSM152875 4 0.5119 0.3797 0.112 0.000 0.124 0.764
#> GSM152876 4 0.4834 0.3842 0.096 0.000 0.120 0.784
#> GSM152877 4 0.5332 0.3741 0.128 0.000 0.124 0.748
#> GSM152878 4 0.5332 0.3741 0.128 0.000 0.124 0.748
#> GSM152879 4 0.5332 0.3741 0.128 0.000 0.124 0.748
#> GSM152880 4 0.5332 0.3741 0.128 0.000 0.124 0.748
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.3684 0.6748 0.000 0.720 0.000 0.280 0.000
#> GSM152805 2 0.1701 0.7472 0.016 0.936 0.000 0.048 0.000
#> GSM152806 2 0.1701 0.7472 0.016 0.936 0.000 0.048 0.000
#> GSM152807 2 0.3661 0.6794 0.000 0.724 0.000 0.276 0.000
#> GSM152808 2 0.1701 0.7472 0.016 0.936 0.000 0.048 0.000
#> GSM152809 2 0.3661 0.6794 0.000 0.724 0.000 0.276 0.000
#> GSM152810 5 0.0000 0.0000 0.000 0.000 0.000 0.000 1.000
#> GSM152811 2 0.1701 0.7472 0.016 0.936 0.000 0.048 0.000
#> GSM152812 2 0.3661 0.6794 0.000 0.724 0.000 0.276 0.000
#> GSM152813 2 0.3661 0.6794 0.000 0.724 0.000 0.276 0.000
#> GSM152814 2 0.3661 0.6794 0.000 0.724 0.000 0.276 0.000
#> GSM152815 2 0.3661 0.6794 0.000 0.724 0.000 0.276 0.000
#> GSM152816 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM152817 2 0.1701 0.7472 0.016 0.936 0.000 0.048 0.000
#> GSM152818 2 0.1701 0.7472 0.016 0.936 0.000 0.048 0.000
#> GSM152819 2 0.0609 0.7922 0.000 0.980 0.000 0.020 0.000
#> GSM152820 2 0.2813 0.7704 0.000 0.832 0.000 0.168 0.000
#> GSM152821 2 0.3508 0.7182 0.000 0.748 0.000 0.252 0.000
#> GSM153115 4 0.4321 0.5010 0.004 0.396 0.000 0.600 0.000
#> GSM153116 2 0.1041 0.7928 0.004 0.964 0.000 0.032 0.000
#> GSM153117 2 0.1270 0.7975 0.000 0.948 0.000 0.052 0.000
#> GSM153118 2 0.2648 0.7767 0.000 0.848 0.000 0.152 0.000
#> GSM153119 2 0.1701 0.7472 0.016 0.936 0.000 0.048 0.000
#> GSM153120 4 0.1701 0.6494 0.016 0.048 0.000 0.936 0.000
#> GSM153121 2 0.0162 0.7892 0.000 0.996 0.000 0.004 0.000
#> GSM153122 2 0.1701 0.7472 0.016 0.936 0.000 0.048 0.000
#> GSM153123 2 0.3003 0.7565 0.000 0.812 0.000 0.188 0.000
#> GSM153124 4 0.4288 0.5277 0.004 0.384 0.000 0.612 0.000
#> GSM153125 4 0.4276 0.5378 0.004 0.380 0.000 0.616 0.000
#> GSM153126 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM153127 2 0.3684 0.6744 0.000 0.720 0.000 0.280 0.000
#> GSM153128 2 0.4375 0.6106 0.016 0.780 0.000 0.056 0.148
#> GSM153129 2 0.1043 0.7968 0.000 0.960 0.000 0.040 0.000
#> GSM153130 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM153131 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM153132 2 0.0703 0.7942 0.000 0.976 0.000 0.024 0.000
#> GSM153133 2 0.3661 0.6926 0.000 0.724 0.000 0.276 0.000
#> GSM153134 2 0.2424 0.7834 0.000 0.868 0.000 0.132 0.000
#> GSM153135 2 0.3661 0.6799 0.000 0.724 0.000 0.276 0.000
#> GSM153136 4 0.2970 0.7679 0.004 0.168 0.000 0.828 0.000
#> GSM153137 4 0.3766 0.7133 0.004 0.268 0.000 0.728 0.000
#> GSM153138 4 0.3969 0.6661 0.004 0.304 0.000 0.692 0.000
#> GSM153139 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM153140 2 0.3684 0.6748 0.000 0.720 0.000 0.280 0.000
#> GSM153141 2 0.3684 0.6744 0.000 0.720 0.000 0.280 0.000
#> GSM153142 2 0.1626 0.7495 0.016 0.940 0.000 0.044 0.000
#> GSM153143 2 0.3730 0.6783 0.000 0.712 0.000 0.288 0.000
#> GSM153144 2 0.1792 0.7958 0.000 0.916 0.000 0.084 0.000
#> GSM153145 2 0.1701 0.7472 0.016 0.936 0.000 0.048 0.000
#> GSM153146 2 0.3586 0.7058 0.000 0.736 0.000 0.264 0.000
#> GSM153147 2 0.3336 0.7290 0.000 0.772 0.000 0.228 0.000
#> GSM153148 2 0.3684 0.6744 0.000 0.720 0.000 0.280 0.000
#> GSM153149 2 0.3586 0.7061 0.000 0.736 0.000 0.264 0.000
#> GSM153150 4 0.2929 0.7588 0.008 0.152 0.000 0.840 0.000
#> GSM153151 2 0.3684 0.6876 0.000 0.720 0.000 0.280 0.000
#> GSM153152 2 0.1732 0.7969 0.000 0.920 0.000 0.080 0.000
#> GSM153153 2 0.2690 0.7767 0.000 0.844 0.000 0.156 0.000
#> GSM153154 2 0.0794 0.7950 0.000 0.972 0.000 0.028 0.000
#> GSM153155 2 0.3796 0.6591 0.000 0.700 0.000 0.300 0.000
#> GSM153156 2 0.0162 0.7892 0.000 0.996 0.000 0.004 0.000
#> GSM153157 2 0.1701 0.7472 0.016 0.936 0.000 0.048 0.000
#> GSM153158 2 0.0703 0.7942 0.000 0.976 0.000 0.024 0.000
#> GSM153159 2 0.1626 0.7495 0.016 0.940 0.000 0.044 0.000
#> GSM153160 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM153161 2 0.3684 0.6744 0.000 0.720 0.000 0.280 0.000
#> GSM153162 2 0.1792 0.7958 0.000 0.916 0.000 0.084 0.000
#> GSM153163 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM153164 2 0.1270 0.7975 0.000 0.948 0.000 0.052 0.000
#> GSM153165 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM153166 2 0.2424 0.7834 0.000 0.868 0.000 0.132 0.000
#> GSM153167 2 0.1121 0.7973 0.000 0.956 0.000 0.044 0.000
#> GSM153168 2 0.1701 0.7472 0.016 0.936 0.000 0.048 0.000
#> GSM153169 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM153170 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM153171 4 0.4321 0.5010 0.004 0.396 0.000 0.600 0.000
#> GSM153172 2 0.2690 0.7749 0.000 0.844 0.000 0.156 0.000
#> GSM153173 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM153174 2 0.1792 0.7958 0.000 0.916 0.000 0.084 0.000
#> GSM153175 4 0.4225 0.5729 0.004 0.364 0.000 0.632 0.000
#> GSM153176 2 0.3913 0.5412 0.000 0.676 0.000 0.324 0.000
#> GSM153177 2 0.2424 0.7834 0.000 0.868 0.000 0.132 0.000
#> GSM152931 4 0.3398 0.7625 0.004 0.216 0.000 0.780 0.000
#> GSM152932 2 0.2648 0.7757 0.000 0.848 0.000 0.152 0.000
#> GSM152933 2 0.2648 0.7767 0.000 0.848 0.000 0.152 0.000
#> GSM152934 4 0.4375 0.3633 0.004 0.420 0.000 0.576 0.000
#> GSM152935 2 0.2230 0.7895 0.000 0.884 0.000 0.116 0.000
#> GSM152936 4 0.2929 0.7588 0.008 0.152 0.000 0.840 0.000
#> GSM152937 2 0.4375 0.6106 0.016 0.780 0.000 0.056 0.148
#> GSM152938 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM152939 4 0.3814 0.7105 0.004 0.276 0.000 0.720 0.000
#> GSM152940 4 0.1701 0.6494 0.016 0.048 0.000 0.936 0.000
#> GSM152941 4 0.6032 -0.3291 0.388 0.000 0.120 0.492 0.000
#> GSM152942 2 0.0963 0.7964 0.000 0.964 0.000 0.036 0.000
#> GSM152943 4 0.4375 0.3633 0.004 0.420 0.000 0.576 0.000
#> GSM152944 2 0.0404 0.7915 0.000 0.988 0.000 0.012 0.000
#> GSM152945 2 0.3586 0.6934 0.000 0.736 0.000 0.264 0.000
#> GSM152946 2 0.3684 0.6748 0.000 0.720 0.000 0.280 0.000
#> GSM152947 4 0.3160 0.7691 0.004 0.188 0.000 0.808 0.000
#> GSM152948 2 0.3684 0.6748 0.000 0.720 0.000 0.280 0.000
#> GSM152949 2 0.1197 0.7985 0.000 0.952 0.000 0.048 0.000
#> GSM152950 2 0.1608 0.7973 0.000 0.928 0.000 0.072 0.000
#> GSM152951 2 0.3730 0.6633 0.000 0.712 0.000 0.288 0.000
#> GSM152952 2 0.3684 0.6744 0.000 0.720 0.000 0.280 0.000
#> GSM152953 2 0.3684 0.6744 0.000 0.720 0.000 0.280 0.000
#> GSM152954 4 0.2929 0.7588 0.008 0.152 0.000 0.840 0.000
#> GSM152955 2 0.4030 0.5321 0.000 0.648 0.000 0.352 0.000
#> GSM152956 2 0.3684 0.6744 0.000 0.720 0.000 0.280 0.000
#> GSM152957 4 0.2818 0.7415 0.012 0.132 0.000 0.856 0.000
#> GSM152958 4 0.2193 0.7080 0.008 0.092 0.000 0.900 0.000
#> GSM152959 4 0.2351 0.6977 0.016 0.088 0.000 0.896 0.000
#> GSM152960 4 0.3171 0.7602 0.008 0.176 0.000 0.816 0.000
#> GSM152961 4 0.1701 0.6494 0.016 0.048 0.000 0.936 0.000
#> GSM152962 2 0.3561 0.7109 0.000 0.740 0.000 0.260 0.000
#> GSM152963 2 0.3684 0.6744 0.000 0.720 0.000 0.280 0.000
#> GSM152964 2 0.4375 0.6106 0.016 0.780 0.000 0.056 0.148
#> GSM152965 2 0.3661 0.6927 0.000 0.724 0.000 0.276 0.000
#> GSM152966 4 0.2890 0.7660 0.004 0.160 0.000 0.836 0.000
#> GSM152967 2 0.3480 0.7059 0.000 0.752 0.000 0.248 0.000
#> GSM152968 2 0.0794 0.7950 0.000 0.972 0.000 0.028 0.000
#> GSM152969 4 0.2890 0.7660 0.004 0.160 0.000 0.836 0.000
#> GSM152970 4 0.1774 0.6556 0.016 0.052 0.000 0.932 0.000
#> GSM152971 4 0.2930 0.7672 0.004 0.164 0.000 0.832 0.000
#> GSM152972 4 0.2848 0.7644 0.004 0.156 0.000 0.840 0.000
#> GSM152973 2 0.3684 0.6355 0.000 0.720 0.000 0.280 0.000
#> GSM152974 2 0.2516 0.7805 0.000 0.860 0.000 0.140 0.000
#> GSM152975 4 0.4450 0.1563 0.004 0.488 0.000 0.508 0.000
#> GSM152976 2 0.4449 -0.0842 0.004 0.512 0.000 0.484 0.000
#> GSM152977 4 0.4108 0.6620 0.008 0.308 0.000 0.684 0.000
#> GSM152978 4 0.1701 0.6494 0.016 0.048 0.000 0.936 0.000
#> GSM152979 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM152980 2 0.3837 0.6455 0.000 0.692 0.000 0.308 0.000
#> GSM152981 2 0.1701 0.7472 0.016 0.936 0.000 0.048 0.000
#> GSM152982 4 0.4288 0.5251 0.004 0.384 0.000 0.612 0.000
#> GSM152983 4 0.4288 0.5251 0.004 0.384 0.000 0.612 0.000
#> GSM152984 2 0.3707 0.6303 0.000 0.716 0.000 0.284 0.000
#> GSM152985 4 0.1701 0.6494 0.016 0.048 0.000 0.936 0.000
#> GSM152986 4 0.2674 0.7539 0.004 0.140 0.000 0.856 0.000
#> GSM152987 1 0.5393 0.2580 0.504 0.000 0.056 0.440 0.000
#> GSM152988 4 0.4135 0.6258 0.004 0.340 0.000 0.656 0.000
#> GSM152989 4 0.2351 0.6977 0.016 0.088 0.000 0.896 0.000
#> GSM152990 2 0.0000 0.7876 0.000 1.000 0.000 0.000 0.000
#> GSM152991 2 0.1701 0.7472 0.016 0.936 0.000 0.048 0.000
#> GSM187524 3 0.0162 0.9069 0.004 0.000 0.996 0.000 0.000
#> GSM187525 3 0.0000 0.9085 0.000 0.000 1.000 0.000 0.000
#> GSM187526 3 0.0000 0.9085 0.000 0.000 1.000 0.000 0.000
#> GSM187527 1 0.3809 0.6100 0.736 0.008 0.000 0.256 0.000
#> GSM152856 1 0.1043 0.8821 0.960 0.000 0.000 0.040 0.000
#> GSM152857 1 0.4113 0.6474 0.784 0.076 0.000 0.140 0.000
#> GSM152858 3 0.1197 0.9325 0.048 0.000 0.952 0.000 0.000
#> GSM152859 3 0.4579 0.4646 0.016 0.000 0.668 0.008 0.308
#> GSM152860 3 0.1197 0.9325 0.048 0.000 0.952 0.000 0.000
#> GSM152861 1 0.2236 0.8711 0.908 0.000 0.068 0.024 0.000
#> GSM152862 3 0.1197 0.9325 0.048 0.000 0.952 0.000 0.000
#> GSM152863 1 0.2520 0.8744 0.896 0.000 0.056 0.048 0.000
#> GSM152864 1 0.2236 0.8711 0.908 0.000 0.068 0.024 0.000
#> GSM152865 1 0.2236 0.8711 0.908 0.000 0.068 0.024 0.000
#> GSM152866 1 0.3877 0.7310 0.764 0.000 0.212 0.024 0.000
#> GSM152867 1 0.2236 0.8711 0.908 0.000 0.068 0.024 0.000
#> GSM152868 1 0.2236 0.8711 0.908 0.000 0.068 0.024 0.000
#> GSM152869 1 0.2236 0.8711 0.908 0.000 0.068 0.024 0.000
#> GSM152870 3 0.1197 0.9325 0.048 0.000 0.952 0.000 0.000
#> GSM152871 3 0.1197 0.9325 0.048 0.000 0.952 0.000 0.000
#> GSM152872 3 0.1197 0.9325 0.048 0.000 0.952 0.000 0.000
#> GSM152873 1 0.1043 0.8821 0.960 0.000 0.000 0.040 0.000
#> GSM152874 1 0.1043 0.8821 0.960 0.000 0.000 0.040 0.000
#> GSM152875 1 0.1341 0.8747 0.944 0.000 0.000 0.056 0.000
#> GSM152876 1 0.1671 0.8589 0.924 0.000 0.000 0.076 0.000
#> GSM152877 1 0.1043 0.8821 0.960 0.000 0.000 0.040 0.000
#> GSM152878 1 0.1043 0.8821 0.960 0.000 0.000 0.040 0.000
#> GSM152879 1 0.1043 0.8821 0.960 0.000 0.000 0.040 0.000
#> GSM152880 1 0.1043 0.8821 0.960 0.000 0.000 0.040 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.0937 0.638 0.000 0.960 0.000 0.040 0.000 NA
#> GSM152805 2 0.3847 0.606 0.000 0.544 0.000 0.000 0.456 NA
#> GSM152806 2 0.3847 0.606 0.000 0.544 0.000 0.000 0.456 NA
#> GSM152807 2 0.0865 0.641 0.000 0.964 0.000 0.036 0.000 NA
#> GSM152808 2 0.3847 0.606 0.000 0.544 0.000 0.000 0.456 NA
#> GSM152809 2 0.0865 0.641 0.000 0.964 0.000 0.036 0.000 NA
#> GSM152810 5 0.3862 0.000 0.000 0.000 0.000 0.000 0.524 NA
#> GSM152811 2 0.3847 0.606 0.000 0.544 0.000 0.000 0.456 NA
#> GSM152812 2 0.0865 0.641 0.000 0.964 0.000 0.036 0.000 NA
#> GSM152813 2 0.0865 0.641 0.000 0.964 0.000 0.036 0.000 NA
#> GSM152814 2 0.0865 0.641 0.000 0.964 0.000 0.036 0.000 NA
#> GSM152815 2 0.0865 0.641 0.000 0.964 0.000 0.036 0.000 NA
#> GSM152816 2 0.3371 0.702 0.000 0.708 0.000 0.000 0.292 NA
#> GSM152817 2 0.3847 0.606 0.000 0.544 0.000 0.000 0.456 NA
#> GSM152818 2 0.3847 0.606 0.000 0.544 0.000 0.000 0.456 NA
#> GSM152819 2 0.3371 0.704 0.000 0.708 0.000 0.000 0.292 NA
#> GSM152820 2 0.2783 0.704 0.000 0.836 0.000 0.016 0.148 NA
#> GSM152821 2 0.1700 0.671 0.000 0.928 0.000 0.024 0.048 NA
#> GSM153115 2 0.3706 -0.281 0.000 0.620 0.000 0.380 0.000 NA
#> GSM153116 2 0.3371 0.704 0.000 0.708 0.000 0.000 0.292 NA
#> GSM153117 2 0.3163 0.715 0.000 0.764 0.000 0.004 0.232 NA
#> GSM153118 2 0.2165 0.709 0.000 0.884 0.000 0.008 0.108 NA
#> GSM153119 2 0.3843 0.610 0.000 0.548 0.000 0.000 0.452 NA
#> GSM153120 4 0.3151 0.806 0.000 0.252 0.000 0.748 0.000 NA
#> GSM153121 2 0.3409 0.700 0.000 0.700 0.000 0.000 0.300 NA
#> GSM153122 2 0.3847 0.606 0.000 0.544 0.000 0.000 0.456 NA
#> GSM153123 2 0.2094 0.694 0.000 0.900 0.000 0.020 0.080 NA
#> GSM153124 2 0.3747 -0.320 0.000 0.604 0.000 0.396 0.000 NA
#> GSM153125 2 0.3756 -0.334 0.000 0.600 0.000 0.400 0.000 NA
#> GSM153126 2 0.3515 0.689 0.000 0.676 0.000 0.000 0.324 NA
#> GSM153127 2 0.0937 0.638 0.000 0.960 0.000 0.040 0.000 NA
#> GSM153128 2 0.4705 0.490 0.000 0.480 0.000 0.000 0.476 NA
#> GSM153129 2 0.3215 0.713 0.000 0.756 0.000 0.004 0.240 NA
#> GSM153130 2 0.3390 0.700 0.000 0.704 0.000 0.000 0.296 NA
#> GSM153131 2 0.3371 0.702 0.000 0.708 0.000 0.000 0.292 NA
#> GSM153132 2 0.3288 0.707 0.000 0.724 0.000 0.000 0.276 NA
#> GSM153133 2 0.1575 0.655 0.000 0.936 0.000 0.032 0.032 NA
#> GSM153134 2 0.2790 0.710 0.000 0.840 0.000 0.020 0.140 NA
#> GSM153135 2 0.0865 0.642 0.000 0.964 0.000 0.036 0.000 NA
#> GSM153136 4 0.3727 0.833 0.000 0.388 0.000 0.612 0.000 NA
#> GSM153137 4 0.3868 0.660 0.000 0.492 0.000 0.508 0.000 NA
#> GSM153138 2 0.3854 -0.575 0.000 0.536 0.000 0.464 0.000 NA
#> GSM153139 2 0.3390 0.700 0.000 0.704 0.000 0.000 0.296 NA
#> GSM153140 2 0.0937 0.638 0.000 0.960 0.000 0.040 0.000 NA
#> GSM153141 2 0.0937 0.638 0.000 0.960 0.000 0.040 0.000 NA
#> GSM153142 2 0.3810 0.626 0.000 0.572 0.000 0.000 0.428 NA
#> GSM153143 2 0.1480 0.641 0.000 0.940 0.000 0.040 0.020 NA
#> GSM153144 2 0.2703 0.716 0.000 0.824 0.000 0.004 0.172 NA
#> GSM153145 2 0.3847 0.606 0.000 0.544 0.000 0.000 0.456 NA
#> GSM153146 2 0.1644 0.663 0.000 0.932 0.000 0.028 0.040 NA
#> GSM153147 2 0.1926 0.682 0.000 0.912 0.000 0.020 0.068 NA
#> GSM153148 2 0.0937 0.638 0.000 0.960 0.000 0.040 0.000 NA
#> GSM153149 2 0.1492 0.664 0.000 0.940 0.000 0.024 0.036 NA
#> GSM153150 4 0.3672 0.838 0.000 0.368 0.000 0.632 0.000 NA
#> GSM153151 2 0.1649 0.652 0.000 0.932 0.000 0.036 0.032 NA
#> GSM153152 2 0.2964 0.717 0.000 0.792 0.000 0.004 0.204 NA
#> GSM153153 2 0.2358 0.707 0.000 0.876 0.000 0.016 0.108 NA
#> GSM153154 2 0.3266 0.708 0.000 0.728 0.000 0.000 0.272 NA
#> GSM153155 2 0.1682 0.628 0.000 0.928 0.000 0.052 0.020 NA
#> GSM153156 2 0.3409 0.700 0.000 0.700 0.000 0.000 0.300 NA
#> GSM153157 2 0.3838 0.612 0.000 0.552 0.000 0.000 0.448 NA
#> GSM153158 2 0.3309 0.706 0.000 0.720 0.000 0.000 0.280 NA
#> GSM153159 2 0.3804 0.629 0.000 0.576 0.000 0.000 0.424 NA
#> GSM153160 2 0.3390 0.700 0.000 0.704 0.000 0.000 0.296 NA
#> GSM153161 2 0.0937 0.638 0.000 0.960 0.000 0.040 0.000 NA
#> GSM153162 2 0.2738 0.716 0.000 0.820 0.000 0.004 0.176 NA
#> GSM153163 2 0.3390 0.700 0.000 0.704 0.000 0.000 0.296 NA
#> GSM153164 2 0.3109 0.716 0.000 0.772 0.000 0.004 0.224 NA
#> GSM153165 2 0.3390 0.700 0.000 0.704 0.000 0.000 0.296 NA
#> GSM153166 2 0.2790 0.710 0.000 0.840 0.000 0.020 0.140 NA
#> GSM153167 2 0.3189 0.714 0.000 0.760 0.000 0.004 0.236 NA
#> GSM153168 2 0.3847 0.606 0.000 0.544 0.000 0.000 0.456 NA
#> GSM153169 2 0.3446 0.696 0.000 0.692 0.000 0.000 0.308 NA
#> GSM153170 2 0.3390 0.700 0.000 0.704 0.000 0.000 0.296 NA
#> GSM153171 2 0.3706 -0.281 0.000 0.620 0.000 0.380 0.000 NA
#> GSM153172 2 0.2170 0.705 0.000 0.888 0.000 0.012 0.100 NA
#> GSM153173 2 0.3390 0.700 0.000 0.704 0.000 0.000 0.296 NA
#> GSM153174 2 0.2703 0.716 0.000 0.824 0.000 0.004 0.172 NA
#> GSM153175 2 0.3789 -0.383 0.000 0.584 0.000 0.416 0.000 NA
#> GSM153176 2 0.3754 0.550 0.000 0.776 0.000 0.152 0.072 NA
#> GSM153177 2 0.2790 0.710 0.000 0.840 0.000 0.020 0.140 NA
#> GSM152931 4 0.3823 0.765 0.000 0.436 0.000 0.564 0.000 NA
#> GSM152932 2 0.2536 0.706 0.000 0.864 0.000 0.020 0.116 NA
#> GSM152933 2 0.2165 0.709 0.000 0.884 0.000 0.008 0.108 NA
#> GSM152934 2 0.4092 -0.147 0.000 0.636 0.000 0.344 0.020 NA
#> GSM152935 2 0.2340 0.715 0.000 0.852 0.000 0.000 0.148 NA
#> GSM152936 4 0.3672 0.838 0.000 0.368 0.000 0.632 0.000 NA
#> GSM152937 2 0.4705 0.490 0.000 0.480 0.000 0.000 0.476 NA
#> GSM152938 2 0.3371 0.702 0.000 0.708 0.000 0.000 0.292 NA
#> GSM152939 2 0.3868 -0.632 0.000 0.504 0.000 0.496 0.000 NA
#> GSM152940 4 0.3151 0.806 0.000 0.252 0.000 0.748 0.000 NA
#> GSM152941 4 0.7319 -0.145 0.144 0.060 0.160 0.548 0.008 NA
#> GSM152942 2 0.3126 0.712 0.000 0.752 0.000 0.000 0.248 NA
#> GSM152943 2 0.4092 -0.147 0.000 0.636 0.000 0.344 0.020 NA
#> GSM152944 2 0.3371 0.703 0.000 0.708 0.000 0.000 0.292 NA
#> GSM152945 2 0.1049 0.651 0.000 0.960 0.000 0.032 0.008 NA
#> GSM152946 2 0.0937 0.638 0.000 0.960 0.000 0.040 0.000 NA
#> GSM152947 4 0.3774 0.805 0.000 0.408 0.000 0.592 0.000 NA
#> GSM152948 2 0.0937 0.638 0.000 0.960 0.000 0.040 0.000 NA
#> GSM152949 2 0.3076 0.715 0.000 0.760 0.000 0.000 0.240 NA
#> GSM152950 2 0.3109 0.716 0.000 0.772 0.000 0.004 0.224 NA
#> GSM152951 2 0.1075 0.632 0.000 0.952 0.000 0.048 0.000 NA
#> GSM152952 2 0.0937 0.638 0.000 0.960 0.000 0.040 0.000 NA
#> GSM152953 2 0.0937 0.638 0.000 0.960 0.000 0.040 0.000 NA
#> GSM152954 4 0.3672 0.838 0.000 0.368 0.000 0.632 0.000 NA
#> GSM152955 2 0.2536 0.555 0.000 0.864 0.000 0.116 0.020 NA
#> GSM152956 2 0.0937 0.638 0.000 0.960 0.000 0.040 0.000 NA
#> GSM152957 4 0.3578 0.838 0.000 0.340 0.000 0.660 0.000 NA
#> GSM152958 4 0.3428 0.834 0.000 0.304 0.000 0.696 0.000 NA
#> GSM152959 4 0.3371 0.828 0.000 0.292 0.000 0.708 0.000 NA
#> GSM152960 4 0.3737 0.812 0.000 0.392 0.000 0.608 0.000 NA
#> GSM152961 4 0.3151 0.806 0.000 0.252 0.000 0.748 0.000 NA
#> GSM152962 2 0.1765 0.667 0.000 0.924 0.000 0.024 0.052 NA
#> GSM152963 2 0.0937 0.638 0.000 0.960 0.000 0.040 0.000 NA
#> GSM152964 2 0.4705 0.490 0.000 0.480 0.000 0.000 0.476 NA
#> GSM152965 2 0.1575 0.655 0.000 0.936 0.000 0.032 0.032 NA
#> GSM152966 4 0.3706 0.838 0.000 0.380 0.000 0.620 0.000 NA
#> GSM152967 2 0.2265 0.664 0.000 0.896 0.000 0.052 0.052 NA
#> GSM152968 2 0.3266 0.708 0.000 0.728 0.000 0.000 0.272 NA
#> GSM152969 4 0.3706 0.838 0.000 0.380 0.000 0.620 0.000 NA
#> GSM152970 4 0.3198 0.812 0.000 0.260 0.000 0.740 0.000 NA
#> GSM152971 4 0.3717 0.835 0.000 0.384 0.000 0.616 0.000 NA
#> GSM152972 4 0.3695 0.839 0.000 0.376 0.000 0.624 0.000 NA
#> GSM152973 2 0.3396 0.607 0.000 0.812 0.000 0.116 0.072 NA
#> GSM152974 2 0.2709 0.709 0.000 0.848 0.000 0.020 0.132 NA
#> GSM152975 2 0.3448 0.121 0.000 0.716 0.000 0.280 0.004 NA
#> GSM152976 2 0.4009 0.156 0.000 0.684 0.000 0.288 0.028 NA
#> GSM152977 2 0.3991 -0.552 0.000 0.524 0.000 0.472 0.004 NA
#> GSM152978 4 0.3151 0.806 0.000 0.252 0.000 0.748 0.000 NA
#> GSM152979 2 0.3390 0.700 0.000 0.704 0.000 0.000 0.296 NA
#> GSM152980 2 0.1807 0.623 0.000 0.920 0.000 0.060 0.020 NA
#> GSM152981 2 0.3847 0.606 0.000 0.544 0.000 0.000 0.456 NA
#> GSM152982 2 0.3881 -0.321 0.000 0.600 0.000 0.396 0.004 NA
#> GSM152983 2 0.3881 -0.321 0.000 0.600 0.000 0.396 0.004 NA
#> GSM152984 2 0.3341 0.604 0.000 0.816 0.000 0.116 0.068 NA
#> GSM152985 4 0.3151 0.806 0.000 0.252 0.000 0.748 0.000 NA
#> GSM152986 4 0.3647 0.841 0.000 0.360 0.000 0.640 0.000 NA
#> GSM152987 4 0.6050 -0.330 0.160 0.000 0.096 0.636 0.012 NA
#> GSM152988 2 0.3950 -0.461 0.000 0.564 0.000 0.432 0.004 NA
#> GSM152989 4 0.3371 0.828 0.000 0.292 0.000 0.708 0.000 NA
#> GSM152990 2 0.3390 0.700 0.000 0.704 0.000 0.000 0.296 NA
#> GSM152991 2 0.3828 0.619 0.000 0.560 0.000 0.000 0.440 NA
#> GSM187524 3 0.1644 0.886 0.000 0.000 0.932 0.028 0.000 NA
#> GSM187525 3 0.1572 0.888 0.000 0.000 0.936 0.028 0.000 NA
#> GSM187526 3 0.1572 0.888 0.000 0.000 0.936 0.028 0.000 NA
#> GSM187527 1 0.4415 0.657 0.760 0.052 0.000 0.132 0.000 NA
#> GSM152856 1 0.0260 0.901 0.992 0.000 0.000 0.008 0.000 NA
#> GSM152857 1 0.4057 0.737 0.812 0.056 0.000 0.020 0.040 NA
#> GSM152858 3 0.0000 0.915 0.000 0.000 1.000 0.000 0.000 NA
#> GSM152859 3 0.5035 0.208 0.008 0.000 0.472 0.052 0.000 NA
#> GSM152860 3 0.0000 0.915 0.000 0.000 1.000 0.000 0.000 NA
#> GSM152861 1 0.2400 0.879 0.872 0.000 0.116 0.008 0.000 NA
#> GSM152862 3 0.0000 0.915 0.000 0.000 1.000 0.000 0.000 NA
#> GSM152863 1 0.2207 0.891 0.900 0.000 0.076 0.008 0.000 NA
#> GSM152864 1 0.2400 0.879 0.872 0.000 0.116 0.008 0.000 NA
#> GSM152865 1 0.2400 0.879 0.872 0.000 0.116 0.008 0.000 NA
#> GSM152866 1 0.3827 0.746 0.752 0.000 0.212 0.012 0.000 NA
#> GSM152867 1 0.2400 0.879 0.872 0.000 0.116 0.008 0.000 NA
#> GSM152868 1 0.2400 0.879 0.872 0.000 0.116 0.008 0.000 NA
#> GSM152869 1 0.2400 0.879 0.872 0.000 0.116 0.008 0.000 NA
#> GSM152870 3 0.0000 0.915 0.000 0.000 1.000 0.000 0.000 NA
#> GSM152871 3 0.0000 0.915 0.000 0.000 1.000 0.000 0.000 NA
#> GSM152872 3 0.0000 0.915 0.000 0.000 1.000 0.000 0.000 NA
#> GSM152873 1 0.0260 0.901 0.992 0.000 0.000 0.008 0.000 NA
#> GSM152874 1 0.0260 0.901 0.992 0.000 0.000 0.008 0.000 NA
#> GSM152875 1 0.0717 0.895 0.976 0.000 0.000 0.008 0.000 NA
#> GSM152876 1 0.1168 0.885 0.956 0.000 0.000 0.016 0.000 NA
#> GSM152877 1 0.0260 0.901 0.992 0.000 0.000 0.008 0.000 NA
#> GSM152878 1 0.0260 0.901 0.992 0.000 0.000 0.008 0.000 NA
#> GSM152879 1 0.0260 0.901 0.992 0.000 0.000 0.008 0.000 NA
#> GSM152880 1 0.0260 0.901 0.992 0.000 0.000 0.008 0.000 NA
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> ATC:hclust 162 2.13e-27 2
#> ATC:hclust 122 1.10e-18 3
#> ATC:hclust 124 1.20e-19 4
#> ATC:hclust 163 1.78e-30 5
#> ATC:hclust 149 6.72e-29 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "kmeans"]
# you can also extract it by
# res = res_list["ATC:kmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.996 0.998 0.3131 0.687 0.687
#> 3 3 0.790 0.885 0.915 0.9322 0.666 0.517
#> 4 4 0.645 0.751 0.784 0.1680 0.798 0.509
#> 5 5 0.677 0.667 0.801 0.0741 0.967 0.874
#> 6 6 0.697 0.618 0.769 0.0480 0.898 0.622
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.999 0.000 1.000
#> GSM152805 2 0.0000 0.999 0.000 1.000
#> GSM152806 2 0.0000 0.999 0.000 1.000
#> GSM152807 2 0.0000 0.999 0.000 1.000
#> GSM152808 2 0.0000 0.999 0.000 1.000
#> GSM152809 2 0.0000 0.999 0.000 1.000
#> GSM152810 2 0.0000 0.999 0.000 1.000
#> GSM152811 2 0.0000 0.999 0.000 1.000
#> GSM152812 2 0.0000 0.999 0.000 1.000
#> GSM152813 2 0.0000 0.999 0.000 1.000
#> GSM152814 2 0.0000 0.999 0.000 1.000
#> GSM152815 2 0.0000 0.999 0.000 1.000
#> GSM152816 2 0.0000 0.999 0.000 1.000
#> GSM152817 2 0.0000 0.999 0.000 1.000
#> GSM152818 2 0.0000 0.999 0.000 1.000
#> GSM152819 2 0.0000 0.999 0.000 1.000
#> GSM152820 2 0.0000 0.999 0.000 1.000
#> GSM152821 2 0.0000 0.999 0.000 1.000
#> GSM153115 2 0.0000 0.999 0.000 1.000
#> GSM153116 2 0.0000 0.999 0.000 1.000
#> GSM153117 2 0.0000 0.999 0.000 1.000
#> GSM153118 2 0.0000 0.999 0.000 1.000
#> GSM153119 2 0.0000 0.999 0.000 1.000
#> GSM153120 2 0.0000 0.999 0.000 1.000
#> GSM153121 2 0.0000 0.999 0.000 1.000
#> GSM153122 2 0.0000 0.999 0.000 1.000
#> GSM153123 2 0.0000 0.999 0.000 1.000
#> GSM153124 2 0.0000 0.999 0.000 1.000
#> GSM153125 2 0.0000 0.999 0.000 1.000
#> GSM153126 2 0.0000 0.999 0.000 1.000
#> GSM153127 2 0.0000 0.999 0.000 1.000
#> GSM153128 2 0.0000 0.999 0.000 1.000
#> GSM153129 2 0.0000 0.999 0.000 1.000
#> GSM153130 2 0.0000 0.999 0.000 1.000
#> GSM153131 2 0.0000 0.999 0.000 1.000
#> GSM153132 2 0.0000 0.999 0.000 1.000
#> GSM153133 2 0.0000 0.999 0.000 1.000
#> GSM153134 2 0.0000 0.999 0.000 1.000
#> GSM153135 2 0.0000 0.999 0.000 1.000
#> GSM153136 2 0.0000 0.999 0.000 1.000
#> GSM153137 2 0.0000 0.999 0.000 1.000
#> GSM153138 2 0.0000 0.999 0.000 1.000
#> GSM153139 2 0.0000 0.999 0.000 1.000
#> GSM153140 2 0.0000 0.999 0.000 1.000
#> GSM153141 2 0.0000 0.999 0.000 1.000
#> GSM153142 2 0.0000 0.999 0.000 1.000
#> GSM153143 2 0.0000 0.999 0.000 1.000
#> GSM153144 2 0.0000 0.999 0.000 1.000
#> GSM153145 2 0.0000 0.999 0.000 1.000
#> GSM153146 2 0.0000 0.999 0.000 1.000
#> GSM153147 2 0.0000 0.999 0.000 1.000
#> GSM153148 2 0.0000 0.999 0.000 1.000
#> GSM153149 2 0.0000 0.999 0.000 1.000
#> GSM153150 2 0.0000 0.999 0.000 1.000
#> GSM153151 2 0.0000 0.999 0.000 1.000
#> GSM153152 2 0.0000 0.999 0.000 1.000
#> GSM153153 2 0.0000 0.999 0.000 1.000
#> GSM153154 2 0.0000 0.999 0.000 1.000
#> GSM153155 2 0.0000 0.999 0.000 1.000
#> GSM153156 2 0.0000 0.999 0.000 1.000
#> GSM153157 2 0.0000 0.999 0.000 1.000
#> GSM153158 2 0.0000 0.999 0.000 1.000
#> GSM153159 2 0.0000 0.999 0.000 1.000
#> GSM153160 2 0.0000 0.999 0.000 1.000
#> GSM153161 2 0.0000 0.999 0.000 1.000
#> GSM153162 2 0.0000 0.999 0.000 1.000
#> GSM153163 2 0.0000 0.999 0.000 1.000
#> GSM153164 2 0.0000 0.999 0.000 1.000
#> GSM153165 2 0.0000 0.999 0.000 1.000
#> GSM153166 2 0.0000 0.999 0.000 1.000
#> GSM153167 2 0.0000 0.999 0.000 1.000
#> GSM153168 2 0.0000 0.999 0.000 1.000
#> GSM153169 2 0.0000 0.999 0.000 1.000
#> GSM153170 2 0.0000 0.999 0.000 1.000
#> GSM153171 2 0.0000 0.999 0.000 1.000
#> GSM153172 2 0.0000 0.999 0.000 1.000
#> GSM153173 2 0.0000 0.999 0.000 1.000
#> GSM153174 2 0.0000 0.999 0.000 1.000
#> GSM153175 2 0.0000 0.999 0.000 1.000
#> GSM153176 2 0.0000 0.999 0.000 1.000
#> GSM153177 2 0.0000 0.999 0.000 1.000
#> GSM152931 2 0.0000 0.999 0.000 1.000
#> GSM152932 2 0.0000 0.999 0.000 1.000
#> GSM152933 2 0.0000 0.999 0.000 1.000
#> GSM152934 2 0.0000 0.999 0.000 1.000
#> GSM152935 2 0.0000 0.999 0.000 1.000
#> GSM152936 2 0.0000 0.999 0.000 1.000
#> GSM152937 2 0.0000 0.999 0.000 1.000
#> GSM152938 2 0.0000 0.999 0.000 1.000
#> GSM152939 2 0.0000 0.999 0.000 1.000
#> GSM152940 2 0.0000 0.999 0.000 1.000
#> GSM152941 1 0.0000 0.994 1.000 0.000
#> GSM152942 2 0.0000 0.999 0.000 1.000
#> GSM152943 2 0.0000 0.999 0.000 1.000
#> GSM152944 2 0.0000 0.999 0.000 1.000
#> GSM152945 2 0.0000 0.999 0.000 1.000
#> GSM152946 2 0.0000 0.999 0.000 1.000
#> GSM152947 2 0.0000 0.999 0.000 1.000
#> GSM152948 2 0.0000 0.999 0.000 1.000
#> GSM152949 2 0.0000 0.999 0.000 1.000
#> GSM152950 2 0.0000 0.999 0.000 1.000
#> GSM152951 2 0.0000 0.999 0.000 1.000
#> GSM152952 2 0.0000 0.999 0.000 1.000
#> GSM152953 2 0.0000 0.999 0.000 1.000
#> GSM152954 2 0.0000 0.999 0.000 1.000
#> GSM152955 2 0.0000 0.999 0.000 1.000
#> GSM152956 2 0.0000 0.999 0.000 1.000
#> GSM152957 2 0.0000 0.999 0.000 1.000
#> GSM152958 2 0.0000 0.999 0.000 1.000
#> GSM152959 2 0.3879 0.917 0.076 0.924
#> GSM152960 2 0.0000 0.999 0.000 1.000
#> GSM152961 2 0.0000 0.999 0.000 1.000
#> GSM152962 2 0.0000 0.999 0.000 1.000
#> GSM152963 2 0.0000 0.999 0.000 1.000
#> GSM152964 2 0.0000 0.999 0.000 1.000
#> GSM152965 2 0.0000 0.999 0.000 1.000
#> GSM152966 2 0.0000 0.999 0.000 1.000
#> GSM152967 2 0.0000 0.999 0.000 1.000
#> GSM152968 2 0.0000 0.999 0.000 1.000
#> GSM152969 2 0.0000 0.999 0.000 1.000
#> GSM152970 2 0.0000 0.999 0.000 1.000
#> GSM152971 2 0.0000 0.999 0.000 1.000
#> GSM152972 2 0.0000 0.999 0.000 1.000
#> GSM152973 2 0.0000 0.999 0.000 1.000
#> GSM152974 2 0.0000 0.999 0.000 1.000
#> GSM152975 2 0.0000 0.999 0.000 1.000
#> GSM152976 2 0.0000 0.999 0.000 1.000
#> GSM152977 2 0.0000 0.999 0.000 1.000
#> GSM152978 2 0.0000 0.999 0.000 1.000
#> GSM152979 2 0.0000 0.999 0.000 1.000
#> GSM152980 2 0.0000 0.999 0.000 1.000
#> GSM152981 2 0.0000 0.999 0.000 1.000
#> GSM152982 2 0.0000 0.999 0.000 1.000
#> GSM152983 2 0.0000 0.999 0.000 1.000
#> GSM152984 2 0.0000 0.999 0.000 1.000
#> GSM152985 1 0.0376 0.990 0.996 0.004
#> GSM152986 2 0.0000 0.999 0.000 1.000
#> GSM152987 1 0.0000 0.994 1.000 0.000
#> GSM152988 2 0.0000 0.999 0.000 1.000
#> GSM152989 1 0.0000 0.994 1.000 0.000
#> GSM152990 2 0.0000 0.999 0.000 1.000
#> GSM152991 2 0.0000 0.999 0.000 1.000
#> GSM187524 1 0.0000 0.994 1.000 0.000
#> GSM187525 1 0.0000 0.994 1.000 0.000
#> GSM187526 1 0.0000 0.994 1.000 0.000
#> GSM187527 1 0.0000 0.994 1.000 0.000
#> GSM152856 1 0.0000 0.994 1.000 0.000
#> GSM152857 1 0.7219 0.750 0.800 0.200
#> GSM152858 1 0.0000 0.994 1.000 0.000
#> GSM152859 1 0.0000 0.994 1.000 0.000
#> GSM152860 1 0.0000 0.994 1.000 0.000
#> GSM152861 1 0.0000 0.994 1.000 0.000
#> GSM152862 1 0.0000 0.994 1.000 0.000
#> GSM152863 1 0.0000 0.994 1.000 0.000
#> GSM152864 1 0.0000 0.994 1.000 0.000
#> GSM152865 1 0.0000 0.994 1.000 0.000
#> GSM152866 1 0.0000 0.994 1.000 0.000
#> GSM152867 1 0.0000 0.994 1.000 0.000
#> GSM152868 1 0.0000 0.994 1.000 0.000
#> GSM152869 1 0.0000 0.994 1.000 0.000
#> GSM152870 1 0.0000 0.994 1.000 0.000
#> GSM152871 1 0.0000 0.994 1.000 0.000
#> GSM152872 1 0.0000 0.994 1.000 0.000
#> GSM152873 1 0.0000 0.994 1.000 0.000
#> GSM152874 1 0.0000 0.994 1.000 0.000
#> GSM152875 1 0.0000 0.994 1.000 0.000
#> GSM152876 1 0.0000 0.994 1.000 0.000
#> GSM152877 1 0.0000 0.994 1.000 0.000
#> GSM152878 1 0.0000 0.994 1.000 0.000
#> GSM152879 1 0.0000 0.994 1.000 0.000
#> GSM152880 1 0.0000 0.994 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152805 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152806 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152807 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152808 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152809 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152810 3 0.3412 0.814 0.000 0.124 0.876
#> GSM152811 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152812 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152813 2 0.2796 0.865 0.000 0.908 0.092
#> GSM152814 2 0.4346 0.738 0.000 0.816 0.184
#> GSM152815 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152816 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152817 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152818 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152819 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152820 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152821 3 0.6126 0.550 0.000 0.400 0.600
#> GSM153115 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153116 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153117 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153118 2 0.4931 0.649 0.000 0.768 0.232
#> GSM153119 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153120 2 0.1015 0.938 0.012 0.980 0.008
#> GSM153121 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153122 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153123 2 0.4452 0.725 0.000 0.808 0.192
#> GSM153124 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153125 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153126 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153127 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153128 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153129 3 0.5926 0.626 0.000 0.356 0.644
#> GSM153130 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153131 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153132 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153133 3 0.6215 0.481 0.000 0.428 0.572
#> GSM153134 3 0.6095 0.566 0.000 0.392 0.608
#> GSM153135 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153136 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153137 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153138 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153139 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153140 2 0.0424 0.955 0.000 0.992 0.008
#> GSM153141 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153142 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153143 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153144 2 0.4346 0.738 0.000 0.816 0.184
#> GSM153145 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153146 3 0.6126 0.550 0.000 0.400 0.600
#> GSM153147 3 0.5529 0.709 0.000 0.296 0.704
#> GSM153148 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153149 3 0.6026 0.594 0.000 0.376 0.624
#> GSM153150 2 0.0000 0.955 0.000 1.000 0.000
#> GSM153151 3 0.6062 0.580 0.000 0.384 0.616
#> GSM153152 3 0.2711 0.902 0.000 0.088 0.912
#> GSM153153 3 0.6111 0.558 0.000 0.396 0.604
#> GSM153154 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153155 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153156 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153157 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153158 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153159 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153160 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153161 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153162 3 0.3267 0.885 0.000 0.116 0.884
#> GSM153163 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153164 3 0.6095 0.566 0.000 0.392 0.608
#> GSM153165 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153166 3 0.6095 0.566 0.000 0.392 0.608
#> GSM153167 2 0.6126 0.147 0.000 0.600 0.400
#> GSM153168 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153169 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153170 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153171 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153172 2 0.4291 0.744 0.000 0.820 0.180
#> GSM153173 3 0.2625 0.904 0.000 0.084 0.916
#> GSM153174 2 0.4452 0.725 0.000 0.808 0.192
#> GSM153175 2 0.0237 0.958 0.000 0.996 0.004
#> GSM153176 3 0.5254 0.718 0.000 0.264 0.736
#> GSM153177 3 0.6095 0.566 0.000 0.392 0.608
#> GSM152931 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152932 2 0.4702 0.689 0.000 0.788 0.212
#> GSM152933 3 0.6126 0.550 0.000 0.400 0.600
#> GSM152934 2 0.0000 0.955 0.000 1.000 0.000
#> GSM152935 3 0.6095 0.566 0.000 0.392 0.608
#> GSM152936 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152937 3 0.3192 0.883 0.000 0.112 0.888
#> GSM152938 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152939 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152940 2 0.1015 0.938 0.012 0.980 0.008
#> GSM152941 1 0.1129 0.963 0.976 0.004 0.020
#> GSM152942 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152943 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152944 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152945 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152946 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152947 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152948 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152949 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152950 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152951 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152952 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152953 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152954 2 0.0000 0.955 0.000 1.000 0.000
#> GSM152955 2 0.1411 0.929 0.000 0.964 0.036
#> GSM152956 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152957 2 0.0000 0.955 0.000 1.000 0.000
#> GSM152958 2 0.1015 0.938 0.012 0.980 0.008
#> GSM152959 2 0.1482 0.925 0.012 0.968 0.020
#> GSM152960 2 0.0000 0.955 0.000 1.000 0.000
#> GSM152961 2 0.1711 0.916 0.032 0.960 0.008
#> GSM152962 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152963 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152964 3 0.4291 0.825 0.000 0.180 0.820
#> GSM152965 3 0.6126 0.550 0.000 0.400 0.600
#> GSM152966 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152967 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152968 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152969 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152970 2 0.1015 0.938 0.012 0.980 0.008
#> GSM152971 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152972 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152973 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152974 2 0.4796 0.674 0.000 0.780 0.220
#> GSM152975 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152976 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152977 2 0.0000 0.955 0.000 1.000 0.000
#> GSM152978 2 0.1015 0.938 0.012 0.980 0.008
#> GSM152979 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152980 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152981 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152982 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152983 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152984 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152985 2 0.2636 0.883 0.048 0.932 0.020
#> GSM152986 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152987 1 0.1129 0.963 0.976 0.004 0.020
#> GSM152988 2 0.0237 0.958 0.000 0.996 0.004
#> GSM152989 1 0.5200 0.794 0.796 0.184 0.020
#> GSM152990 3 0.2625 0.904 0.000 0.084 0.916
#> GSM152991 3 0.2625 0.904 0.000 0.084 0.916
#> GSM187524 1 0.2772 0.955 0.916 0.004 0.080
#> GSM187525 1 0.2772 0.955 0.916 0.004 0.080
#> GSM187526 1 0.2772 0.955 0.916 0.004 0.080
#> GSM187527 1 0.3989 0.863 0.864 0.124 0.012
#> GSM152856 1 0.0237 0.965 0.996 0.000 0.004
#> GSM152857 1 0.4629 0.788 0.808 0.188 0.004
#> GSM152858 1 0.2772 0.955 0.916 0.004 0.080
#> GSM152859 1 0.2772 0.955 0.916 0.004 0.080
#> GSM152860 1 0.2772 0.955 0.916 0.004 0.080
#> GSM152861 1 0.0592 0.965 0.988 0.000 0.012
#> GSM152862 1 0.2772 0.955 0.916 0.004 0.080
#> GSM152863 1 0.0592 0.965 0.988 0.000 0.012
#> GSM152864 1 0.0592 0.965 0.988 0.000 0.012
#> GSM152865 1 0.0592 0.965 0.988 0.000 0.012
#> GSM152866 1 0.0747 0.965 0.984 0.000 0.016
#> GSM152867 1 0.0000 0.965 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.965 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.965 1.000 0.000 0.000
#> GSM152870 1 0.2772 0.955 0.916 0.004 0.080
#> GSM152871 1 0.2772 0.955 0.916 0.004 0.080
#> GSM152872 1 0.2772 0.955 0.916 0.004 0.080
#> GSM152873 1 0.0237 0.965 0.996 0.000 0.004
#> GSM152874 1 0.0237 0.965 0.996 0.000 0.004
#> GSM152875 1 0.0237 0.965 0.996 0.000 0.004
#> GSM152876 1 0.0237 0.965 0.996 0.000 0.004
#> GSM152877 1 0.0237 0.965 0.996 0.000 0.004
#> GSM152878 1 0.0237 0.965 0.996 0.000 0.004
#> GSM152879 1 0.0237 0.965 0.996 0.000 0.004
#> GSM152880 1 0.0237 0.965 0.996 0.000 0.004
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM152805 3 0.0000 0.8406 0.000 0.000 1.000 0.000
#> GSM152806 3 0.0000 0.8406 0.000 0.000 1.000 0.000
#> GSM152807 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM152808 3 0.0000 0.8406 0.000 0.000 1.000 0.000
#> GSM152809 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM152810 3 0.4054 0.6721 0.000 0.016 0.796 0.188
#> GSM152811 3 0.0469 0.8350 0.000 0.000 0.988 0.012
#> GSM152812 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM152813 2 0.0657 0.6322 0.000 0.984 0.012 0.004
#> GSM152814 2 0.1118 0.6424 0.000 0.964 0.036 0.000
#> GSM152815 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM152816 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM152817 3 0.0000 0.8406 0.000 0.000 1.000 0.000
#> GSM152818 3 0.0000 0.8406 0.000 0.000 1.000 0.000
#> GSM152819 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM152820 3 0.4284 0.8617 0.000 0.224 0.764 0.012
#> GSM152821 2 0.4290 0.5897 0.000 0.800 0.164 0.036
#> GSM153115 4 0.4585 0.9459 0.000 0.332 0.000 0.668
#> GSM153116 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM153117 2 0.5000 -0.3376 0.000 0.504 0.496 0.000
#> GSM153118 2 0.1389 0.6442 0.000 0.952 0.048 0.000
#> GSM153119 3 0.0188 0.8394 0.000 0.000 0.996 0.004
#> GSM153120 4 0.4382 0.9463 0.000 0.296 0.000 0.704
#> GSM153121 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM153122 3 0.0000 0.8406 0.000 0.000 1.000 0.000
#> GSM153123 2 0.1211 0.6434 0.000 0.960 0.040 0.000
#> GSM153124 4 0.4661 0.9278 0.000 0.348 0.000 0.652
#> GSM153125 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM153126 3 0.3528 0.8666 0.000 0.192 0.808 0.000
#> GSM153127 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM153128 3 0.1743 0.8089 0.000 0.004 0.940 0.056
#> GSM153129 2 0.3801 0.5309 0.000 0.780 0.220 0.000
#> GSM153130 3 0.1118 0.8482 0.000 0.036 0.964 0.000
#> GSM153131 3 0.4040 0.8453 0.000 0.248 0.752 0.000
#> GSM153132 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM153133 2 0.4100 0.6076 0.000 0.816 0.148 0.036
#> GSM153134 2 0.3726 0.5475 0.000 0.788 0.212 0.000
#> GSM153135 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM153136 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM153137 4 0.4543 0.9456 0.000 0.324 0.000 0.676
#> GSM153138 2 0.4761 0.0187 0.000 0.628 0.000 0.372
#> GSM153139 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM153140 2 0.3801 0.4812 0.000 0.780 0.000 0.220
#> GSM153141 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM153142 3 0.0000 0.8406 0.000 0.000 1.000 0.000
#> GSM153143 2 0.4008 0.4573 0.000 0.756 0.000 0.244
#> GSM153144 2 0.1118 0.6424 0.000 0.964 0.036 0.000
#> GSM153145 3 0.0000 0.8406 0.000 0.000 1.000 0.000
#> GSM153146 2 0.4290 0.5897 0.000 0.800 0.164 0.036
#> GSM153147 2 0.5021 0.4282 0.000 0.724 0.240 0.036
#> GSM153148 2 0.3801 0.4812 0.000 0.780 0.000 0.220
#> GSM153149 2 0.4466 0.5636 0.000 0.784 0.180 0.036
#> GSM153150 4 0.4382 0.9463 0.000 0.296 0.000 0.704
#> GSM153151 2 0.4290 0.5897 0.000 0.800 0.164 0.036
#> GSM153152 2 0.4730 0.1132 0.000 0.636 0.364 0.000
#> GSM153153 2 0.3400 0.5902 0.000 0.820 0.180 0.000
#> GSM153154 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM153155 2 0.4072 0.4481 0.000 0.748 0.000 0.252
#> GSM153156 3 0.4018 0.8651 0.000 0.224 0.772 0.004
#> GSM153157 3 0.0188 0.8394 0.000 0.000 0.996 0.004
#> GSM153158 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM153159 3 0.0000 0.8406 0.000 0.000 1.000 0.000
#> GSM153160 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM153161 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM153162 2 0.4585 0.2145 0.000 0.668 0.332 0.000
#> GSM153163 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM153164 2 0.3486 0.5787 0.000 0.812 0.188 0.000
#> GSM153165 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM153166 2 0.3649 0.5602 0.000 0.796 0.204 0.000
#> GSM153167 2 0.2647 0.6368 0.000 0.880 0.120 0.000
#> GSM153168 3 0.0000 0.8406 0.000 0.000 1.000 0.000
#> GSM153169 3 0.0336 0.8432 0.000 0.008 0.992 0.000
#> GSM153170 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM153171 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM153172 2 0.1118 0.6424 0.000 0.964 0.036 0.000
#> GSM153173 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM153174 2 0.1211 0.6434 0.000 0.960 0.040 0.000
#> GSM153175 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM153176 3 0.7114 0.6434 0.000 0.252 0.560 0.188
#> GSM153177 2 0.3688 0.5547 0.000 0.792 0.208 0.000
#> GSM152931 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM152932 2 0.1389 0.6442 0.000 0.952 0.048 0.000
#> GSM152933 2 0.3356 0.5947 0.000 0.824 0.176 0.000
#> GSM152934 4 0.4331 0.9328 0.000 0.288 0.000 0.712
#> GSM152935 2 0.3486 0.5787 0.000 0.812 0.188 0.000
#> GSM152936 4 0.4382 0.9463 0.000 0.296 0.000 0.704
#> GSM152937 3 0.2530 0.7766 0.000 0.004 0.896 0.100
#> GSM152938 3 0.3907 0.8606 0.000 0.232 0.768 0.000
#> GSM152939 4 0.4981 0.6962 0.000 0.464 0.000 0.536
#> GSM152940 4 0.4406 0.9473 0.000 0.300 0.000 0.700
#> GSM152941 1 0.2760 0.8536 0.872 0.000 0.000 0.128
#> GSM152942 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM152943 4 0.4356 0.9368 0.000 0.292 0.000 0.708
#> GSM152944 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM152945 2 0.4040 0.4527 0.000 0.752 0.000 0.248
#> GSM152946 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM152947 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM152948 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM152949 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM152950 3 0.4155 0.8530 0.000 0.240 0.756 0.004
#> GSM152951 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM152952 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM152953 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM152954 4 0.4382 0.9463 0.000 0.296 0.000 0.704
#> GSM152955 2 0.5838 -0.2597 0.000 0.524 0.032 0.444
#> GSM152956 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM152957 4 0.4382 0.9463 0.000 0.296 0.000 0.704
#> GSM152958 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM152959 4 0.4356 0.9440 0.000 0.292 0.000 0.708
#> GSM152960 4 0.4331 0.9406 0.000 0.288 0.000 0.712
#> GSM152961 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM152962 3 0.4922 0.8438 0.000 0.228 0.736 0.036
#> GSM152963 2 0.3837 0.4766 0.000 0.776 0.000 0.224
#> GSM152964 3 0.4136 0.6626 0.000 0.016 0.788 0.196
#> GSM152965 2 0.4197 0.5979 0.000 0.808 0.156 0.036
#> GSM152966 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM152967 2 0.3764 0.4854 0.000 0.784 0.000 0.216
#> GSM152968 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM152969 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM152970 4 0.4382 0.9463 0.000 0.296 0.000 0.704
#> GSM152971 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM152972 4 0.4500 0.9496 0.000 0.316 0.000 0.684
#> GSM152973 2 0.0524 0.6258 0.000 0.988 0.004 0.008
#> GSM152974 2 0.1389 0.6442 0.000 0.952 0.048 0.000
#> GSM152975 2 0.3907 0.4582 0.000 0.768 0.000 0.232
#> GSM152976 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM152977 4 0.4331 0.9406 0.000 0.288 0.000 0.712
#> GSM152978 4 0.4382 0.9463 0.000 0.296 0.000 0.704
#> GSM152979 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM152980 4 0.4643 0.9051 0.000 0.344 0.000 0.656
#> GSM152981 3 0.0336 0.8377 0.000 0.000 0.992 0.008
#> GSM152982 4 0.4331 0.9406 0.000 0.288 0.000 0.712
#> GSM152983 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM152984 2 0.2921 0.5444 0.000 0.860 0.000 0.140
#> GSM152985 4 0.4356 0.9440 0.000 0.292 0.000 0.708
#> GSM152986 4 0.4564 0.9492 0.000 0.328 0.000 0.672
#> GSM152987 1 0.1022 0.9101 0.968 0.000 0.000 0.032
#> GSM152988 4 0.4989 0.6756 0.000 0.472 0.000 0.528
#> GSM152989 4 0.6049 0.7442 0.120 0.200 0.000 0.680
#> GSM152990 3 0.3801 0.8671 0.000 0.220 0.780 0.000
#> GSM152991 3 0.0188 0.8394 0.000 0.000 0.996 0.004
#> GSM187524 1 0.3907 0.8689 0.768 0.000 0.000 0.232
#> GSM187525 1 0.3907 0.8689 0.768 0.000 0.000 0.232
#> GSM187526 1 0.3907 0.8689 0.768 0.000 0.000 0.232
#> GSM187527 1 0.4898 0.4449 0.584 0.000 0.000 0.416
#> GSM152856 1 0.1211 0.9102 0.960 0.000 0.000 0.040
#> GSM152857 1 0.5238 0.7459 0.744 0.012 0.040 0.204
#> GSM152858 1 0.3907 0.8689 0.768 0.000 0.000 0.232
#> GSM152859 1 0.4040 0.8621 0.752 0.000 0.000 0.248
#> GSM152860 1 0.3907 0.8689 0.768 0.000 0.000 0.232
#> GSM152861 1 0.0336 0.9123 0.992 0.000 0.000 0.008
#> GSM152862 1 0.3907 0.8689 0.768 0.000 0.000 0.232
#> GSM152863 1 0.0000 0.9127 1.000 0.000 0.000 0.000
#> GSM152864 1 0.0000 0.9127 1.000 0.000 0.000 0.000
#> GSM152865 1 0.0188 0.9125 0.996 0.000 0.000 0.004
#> GSM152866 1 0.1118 0.9106 0.964 0.000 0.000 0.036
#> GSM152867 1 0.0000 0.9127 1.000 0.000 0.000 0.000
#> GSM152868 1 0.0000 0.9127 1.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.9127 1.000 0.000 0.000 0.000
#> GSM152870 1 0.3907 0.8689 0.768 0.000 0.000 0.232
#> GSM152871 1 0.3907 0.8689 0.768 0.000 0.000 0.232
#> GSM152872 1 0.3907 0.8689 0.768 0.000 0.000 0.232
#> GSM152873 1 0.1211 0.9102 0.960 0.000 0.000 0.040
#> GSM152874 1 0.1211 0.9102 0.960 0.000 0.000 0.040
#> GSM152875 1 0.1211 0.9102 0.960 0.000 0.000 0.040
#> GSM152876 1 0.1211 0.9102 0.960 0.000 0.000 0.040
#> GSM152877 1 0.1211 0.9102 0.960 0.000 0.000 0.040
#> GSM152878 1 0.1211 0.9102 0.960 0.000 0.000 0.040
#> GSM152879 1 0.1211 0.9102 0.960 0.000 0.000 0.040
#> GSM152880 1 0.1211 0.9102 0.960 0.000 0.000 0.040
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.3210 0.71930 0.000 0.788 0.000 0.212 0.000
#> GSM152805 3 0.5619 0.39578 0.000 0.156 0.636 0.000 0.208
#> GSM152806 3 0.5619 0.39578 0.000 0.156 0.636 0.000 0.208
#> GSM152807 2 0.3333 0.72274 0.000 0.788 0.004 0.208 0.000
#> GSM152808 3 0.5699 0.37879 0.000 0.156 0.624 0.000 0.220
#> GSM152809 2 0.3210 0.71930 0.000 0.788 0.000 0.212 0.000
#> GSM152810 5 0.7510 0.52944 0.000 0.172 0.244 0.088 0.496
#> GSM152811 3 0.5952 0.30405 0.000 0.164 0.584 0.000 0.252
#> GSM152812 2 0.3210 0.71930 0.000 0.788 0.000 0.212 0.000
#> GSM152813 2 0.3875 0.76904 0.000 0.792 0.160 0.048 0.000
#> GSM152814 2 0.3732 0.76718 0.000 0.792 0.176 0.032 0.000
#> GSM152815 2 0.3210 0.71930 0.000 0.788 0.000 0.212 0.000
#> GSM152816 3 0.0162 0.69897 0.000 0.004 0.996 0.000 0.000
#> GSM152817 3 0.5699 0.37879 0.000 0.156 0.624 0.000 0.220
#> GSM152818 3 0.5619 0.39578 0.000 0.156 0.636 0.000 0.208
#> GSM152819 3 0.0162 0.69897 0.000 0.004 0.996 0.000 0.000
#> GSM152820 3 0.2573 0.61187 0.000 0.016 0.880 0.000 0.104
#> GSM152821 2 0.6215 0.68005 0.000 0.580 0.308 0.048 0.064
#> GSM153115 4 0.2848 0.81717 0.000 0.156 0.000 0.840 0.004
#> GSM153116 3 0.0510 0.70174 0.000 0.000 0.984 0.000 0.016
#> GSM153117 3 0.4283 0.00121 0.000 0.348 0.644 0.000 0.008
#> GSM153118 2 0.4632 0.74170 0.000 0.684 0.284 0.024 0.008
#> GSM153119 3 0.5750 0.36432 0.000 0.156 0.616 0.000 0.228
#> GSM153120 4 0.0671 0.87732 0.000 0.004 0.000 0.980 0.016
#> GSM153121 3 0.1430 0.66672 0.000 0.004 0.944 0.000 0.052
#> GSM153122 3 0.5798 0.35277 0.000 0.156 0.608 0.000 0.236
#> GSM153123 2 0.3829 0.76562 0.000 0.776 0.196 0.028 0.000
#> GSM153124 4 0.2890 0.81416 0.000 0.160 0.000 0.836 0.004
#> GSM153125 4 0.2674 0.83066 0.000 0.140 0.000 0.856 0.004
#> GSM153126 3 0.0807 0.69942 0.000 0.012 0.976 0.000 0.012
#> GSM153127 2 0.3487 0.72017 0.000 0.780 0.000 0.212 0.008
#> GSM153128 5 0.7120 0.43289 0.000 0.164 0.364 0.036 0.436
#> GSM153129 2 0.4738 0.60987 0.000 0.564 0.420 0.012 0.004
#> GSM153130 3 0.4010 0.55873 0.000 0.116 0.796 0.000 0.088
#> GSM153131 3 0.2729 0.59926 0.000 0.060 0.884 0.000 0.056
#> GSM153132 3 0.0451 0.69597 0.000 0.004 0.988 0.000 0.008
#> GSM153133 2 0.6237 0.68338 0.000 0.584 0.300 0.048 0.068
#> GSM153134 2 0.4626 0.68338 0.000 0.616 0.364 0.020 0.000
#> GSM153135 2 0.3487 0.72017 0.000 0.780 0.000 0.212 0.008
#> GSM153136 4 0.1043 0.88372 0.000 0.040 0.000 0.960 0.000
#> GSM153137 4 0.2798 0.82699 0.000 0.140 0.000 0.852 0.008
#> GSM153138 4 0.6099 -0.08725 0.000 0.424 0.000 0.452 0.124
#> GSM153139 3 0.0771 0.70158 0.000 0.004 0.976 0.000 0.020
#> GSM153140 2 0.3421 0.72559 0.000 0.788 0.008 0.204 0.000
#> GSM153141 2 0.3210 0.71930 0.000 0.788 0.000 0.212 0.000
#> GSM153142 3 0.5532 0.40736 0.000 0.156 0.648 0.000 0.196
#> GSM153143 2 0.3779 0.70896 0.000 0.752 0.000 0.236 0.012
#> GSM153144 2 0.3944 0.76564 0.000 0.768 0.200 0.032 0.000
#> GSM153145 3 0.5673 0.38522 0.000 0.156 0.628 0.000 0.216
#> GSM153146 2 0.6269 0.67686 0.000 0.576 0.308 0.048 0.068
#> GSM153147 2 0.6241 0.61395 0.000 0.536 0.360 0.036 0.068
#> GSM153148 2 0.3611 0.72351 0.000 0.780 0.004 0.208 0.008
#> GSM153149 2 0.6392 0.65358 0.000 0.552 0.328 0.048 0.072
#> GSM153150 4 0.0671 0.87732 0.000 0.004 0.000 0.980 0.016
#> GSM153151 2 0.7108 0.58717 0.000 0.488 0.324 0.056 0.132
#> GSM153152 2 0.4968 0.52364 0.000 0.516 0.456 0.000 0.028
#> GSM153153 2 0.4862 0.71292 0.000 0.640 0.328 0.020 0.012
#> GSM153154 3 0.0451 0.69597 0.000 0.004 0.988 0.000 0.008
#> GSM153155 2 0.4904 0.66268 0.000 0.688 0.000 0.240 0.072
#> GSM153156 3 0.2293 0.62992 0.000 0.016 0.900 0.000 0.084
#> GSM153157 3 0.5774 0.35657 0.000 0.156 0.612 0.000 0.232
#> GSM153158 3 0.0510 0.70174 0.000 0.000 0.984 0.000 0.016
#> GSM153159 3 0.5307 0.43389 0.000 0.156 0.676 0.000 0.168
#> GSM153160 3 0.0609 0.70106 0.000 0.000 0.980 0.000 0.020
#> GSM153161 2 0.3487 0.72017 0.000 0.780 0.000 0.212 0.008
#> GSM153162 2 0.4219 0.61140 0.000 0.584 0.416 0.000 0.000
#> GSM153163 3 0.0609 0.70106 0.000 0.000 0.980 0.000 0.020
#> GSM153164 2 0.4895 0.70619 0.000 0.632 0.336 0.020 0.012
#> GSM153165 3 0.0771 0.70158 0.000 0.004 0.976 0.000 0.020
#> GSM153166 2 0.4651 0.67441 0.000 0.608 0.372 0.020 0.000
#> GSM153167 2 0.4895 0.70780 0.000 0.632 0.336 0.020 0.012
#> GSM153168 3 0.5699 0.37879 0.000 0.156 0.624 0.000 0.220
#> GSM153169 3 0.4404 0.51911 0.000 0.152 0.760 0.000 0.088
#> GSM153170 3 0.0162 0.69897 0.000 0.004 0.996 0.000 0.000
#> GSM153171 4 0.2629 0.83351 0.000 0.136 0.000 0.860 0.004
#> GSM153172 2 0.3732 0.76718 0.000 0.792 0.176 0.032 0.000
#> GSM153173 3 0.0609 0.70106 0.000 0.000 0.980 0.000 0.020
#> GSM153174 2 0.4141 0.75788 0.000 0.736 0.236 0.028 0.000
#> GSM153175 4 0.1205 0.88306 0.000 0.040 0.000 0.956 0.004
#> GSM153176 3 0.5355 0.29153 0.000 0.008 0.692 0.160 0.140
#> GSM153177 2 0.4651 0.67441 0.000 0.608 0.372 0.020 0.000
#> GSM152931 4 0.1952 0.86401 0.000 0.084 0.000 0.912 0.004
#> GSM152932 2 0.4114 0.75518 0.000 0.732 0.244 0.024 0.000
#> GSM152933 2 0.4846 0.71485 0.000 0.644 0.324 0.020 0.012
#> GSM152934 4 0.3596 0.73463 0.000 0.016 0.000 0.784 0.200
#> GSM152935 2 0.4895 0.70619 0.000 0.632 0.336 0.020 0.012
#> GSM152936 4 0.0671 0.87732 0.000 0.004 0.000 0.980 0.016
#> GSM152937 5 0.7437 0.49550 0.000 0.168 0.336 0.060 0.436
#> GSM152938 3 0.2124 0.64049 0.000 0.028 0.916 0.000 0.056
#> GSM152939 4 0.4066 0.54636 0.000 0.324 0.000 0.672 0.004
#> GSM152940 4 0.0898 0.88209 0.000 0.020 0.000 0.972 0.008
#> GSM152941 1 0.5380 0.52171 0.644 0.020 0.000 0.288 0.048
#> GSM152942 3 0.0324 0.69777 0.000 0.004 0.992 0.000 0.004
#> GSM152943 4 0.3596 0.73382 0.000 0.016 0.000 0.784 0.200
#> GSM152944 3 0.0609 0.70106 0.000 0.000 0.980 0.000 0.020
#> GSM152945 2 0.4355 0.69147 0.000 0.732 0.000 0.224 0.044
#> GSM152946 2 0.3421 0.72559 0.000 0.788 0.008 0.204 0.000
#> GSM152947 4 0.1331 0.88351 0.000 0.040 0.000 0.952 0.008
#> GSM152948 2 0.3210 0.71930 0.000 0.788 0.000 0.212 0.000
#> GSM152949 3 0.0955 0.68420 0.000 0.004 0.968 0.000 0.028
#> GSM152950 3 0.3033 0.58386 0.000 0.052 0.864 0.000 0.084
#> GSM152951 2 0.3210 0.71930 0.000 0.788 0.000 0.212 0.000
#> GSM152952 2 0.3487 0.72017 0.000 0.780 0.000 0.212 0.008
#> GSM152953 2 0.3487 0.72017 0.000 0.780 0.000 0.212 0.008
#> GSM152954 4 0.0671 0.87732 0.000 0.004 0.000 0.980 0.016
#> GSM152955 4 0.7818 0.14298 0.000 0.240 0.100 0.452 0.208
#> GSM152956 2 0.3487 0.72017 0.000 0.780 0.000 0.212 0.008
#> GSM152957 4 0.0566 0.87828 0.000 0.004 0.000 0.984 0.012
#> GSM152958 4 0.1331 0.88351 0.000 0.040 0.000 0.952 0.008
#> GSM152959 4 0.0898 0.87009 0.000 0.008 0.000 0.972 0.020
#> GSM152960 4 0.2046 0.84573 0.000 0.016 0.000 0.916 0.068
#> GSM152961 4 0.1331 0.88351 0.000 0.040 0.000 0.952 0.008
#> GSM152962 3 0.4482 0.46852 0.000 0.040 0.780 0.036 0.144
#> GSM152963 2 0.3487 0.72017 0.000 0.780 0.000 0.212 0.008
#> GSM152964 5 0.7783 0.52967 0.000 0.164 0.292 0.104 0.440
#> GSM152965 2 0.6664 0.65357 0.000 0.548 0.304 0.056 0.092
#> GSM152966 4 0.1043 0.88372 0.000 0.040 0.000 0.960 0.000
#> GSM152967 2 0.3882 0.72990 0.000 0.776 0.012 0.200 0.012
#> GSM152968 3 0.0771 0.68935 0.000 0.004 0.976 0.000 0.020
#> GSM152969 4 0.1043 0.88372 0.000 0.040 0.000 0.960 0.000
#> GSM152970 4 0.0324 0.87881 0.000 0.004 0.000 0.992 0.004
#> GSM152971 4 0.1043 0.88372 0.000 0.040 0.000 0.960 0.000
#> GSM152972 4 0.1168 0.88384 0.000 0.032 0.000 0.960 0.008
#> GSM152973 2 0.4983 0.74424 0.000 0.680 0.256 0.060 0.004
#> GSM152974 2 0.3845 0.76323 0.000 0.768 0.208 0.024 0.000
#> GSM152975 2 0.3424 0.68930 0.000 0.760 0.000 0.240 0.000
#> GSM152976 4 0.1205 0.88306 0.000 0.040 0.000 0.956 0.004
#> GSM152977 4 0.1106 0.87106 0.000 0.012 0.000 0.964 0.024
#> GSM152978 4 0.0671 0.87732 0.000 0.004 0.000 0.980 0.016
#> GSM152979 3 0.0162 0.69897 0.000 0.004 0.996 0.000 0.000
#> GSM152980 4 0.4916 0.66871 0.000 0.160 0.000 0.716 0.124
#> GSM152981 3 0.5887 0.32098 0.000 0.156 0.592 0.000 0.252
#> GSM152982 4 0.1701 0.85285 0.000 0.016 0.000 0.936 0.048
#> GSM152983 4 0.1043 0.88372 0.000 0.040 0.000 0.960 0.000
#> GSM152984 2 0.5707 0.74003 0.000 0.668 0.164 0.152 0.016
#> GSM152985 4 0.0510 0.87522 0.000 0.000 0.000 0.984 0.016
#> GSM152986 4 0.1205 0.88372 0.000 0.040 0.000 0.956 0.004
#> GSM152987 1 0.4906 0.64317 0.732 0.020 0.000 0.188 0.060
#> GSM152988 4 0.4211 0.45473 0.000 0.360 0.000 0.636 0.004
#> GSM152989 4 0.1865 0.84128 0.008 0.024 0.000 0.936 0.032
#> GSM152990 3 0.0162 0.69897 0.000 0.004 0.996 0.000 0.000
#> GSM152991 3 0.5307 0.43843 0.000 0.156 0.676 0.000 0.168
#> GSM187524 1 0.4802 0.56694 0.504 0.012 0.000 0.004 0.480
#> GSM187525 1 0.4684 0.60110 0.536 0.008 0.000 0.004 0.452
#> GSM187526 1 0.5019 0.60564 0.536 0.024 0.000 0.004 0.436
#> GSM187527 1 0.4802 0.04364 0.504 0.004 0.000 0.480 0.012
#> GSM152856 1 0.0162 0.78110 0.996 0.004 0.000 0.000 0.000
#> GSM152857 1 0.4541 0.57719 0.760 0.004 0.000 0.096 0.140
#> GSM152858 1 0.4291 0.60310 0.536 0.000 0.000 0.000 0.464
#> GSM152859 5 0.4787 -0.61884 0.456 0.012 0.000 0.004 0.528
#> GSM152860 1 0.4291 0.60310 0.536 0.000 0.000 0.000 0.464
#> GSM152861 1 0.1774 0.78331 0.932 0.016 0.000 0.000 0.052
#> GSM152862 1 0.4291 0.60310 0.536 0.000 0.000 0.000 0.464
#> GSM152863 1 0.1774 0.78331 0.932 0.016 0.000 0.000 0.052
#> GSM152864 1 0.1774 0.78331 0.932 0.016 0.000 0.000 0.052
#> GSM152865 1 0.1774 0.78331 0.932 0.016 0.000 0.000 0.052
#> GSM152866 1 0.0000 0.78152 1.000 0.000 0.000 0.000 0.000
#> GSM152867 1 0.1774 0.78331 0.932 0.016 0.000 0.000 0.052
#> GSM152868 1 0.1774 0.78331 0.932 0.016 0.000 0.000 0.052
#> GSM152869 1 0.1774 0.78331 0.932 0.016 0.000 0.000 0.052
#> GSM152870 1 0.4291 0.60310 0.536 0.000 0.000 0.000 0.464
#> GSM152871 1 0.4291 0.60310 0.536 0.000 0.000 0.000 0.464
#> GSM152872 1 0.4291 0.60310 0.536 0.000 0.000 0.000 0.464
#> GSM152873 1 0.0162 0.78110 0.996 0.004 0.000 0.000 0.000
#> GSM152874 1 0.0162 0.78110 0.996 0.004 0.000 0.000 0.000
#> GSM152875 1 0.0162 0.78110 0.996 0.004 0.000 0.000 0.000
#> GSM152876 1 0.0162 0.78110 0.996 0.004 0.000 0.000 0.000
#> GSM152877 1 0.0162 0.78110 0.996 0.004 0.000 0.000 0.000
#> GSM152878 1 0.0162 0.78110 0.996 0.004 0.000 0.000 0.000
#> GSM152879 1 0.0162 0.78110 0.996 0.004 0.000 0.000 0.000
#> GSM152880 1 0.0162 0.78110 0.996 0.004 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.1644 0.757452 0.000 0.920 0.004 0.076 0.000 0.000
#> GSM152805 5 0.3531 0.779327 0.000 0.000 0.328 0.000 0.672 0.000
#> GSM152806 5 0.3499 0.784299 0.000 0.000 0.320 0.000 0.680 0.000
#> GSM152807 2 0.1610 0.755335 0.000 0.916 0.000 0.084 0.000 0.000
#> GSM152808 5 0.3707 0.787568 0.000 0.000 0.312 0.000 0.680 0.008
#> GSM152809 2 0.1806 0.753851 0.000 0.908 0.000 0.088 0.000 0.004
#> GSM152810 5 0.5340 0.425058 0.000 0.028 0.052 0.020 0.652 0.248
#> GSM152811 5 0.4183 0.777306 0.000 0.004 0.268 0.000 0.692 0.036
#> GSM152812 2 0.1806 0.753851 0.000 0.908 0.000 0.088 0.000 0.004
#> GSM152813 2 0.1644 0.734246 0.000 0.920 0.076 0.004 0.000 0.000
#> GSM152814 2 0.1610 0.730247 0.000 0.916 0.084 0.000 0.000 0.000
#> GSM152815 2 0.1663 0.754003 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM152816 3 0.0837 0.667526 0.000 0.004 0.972 0.000 0.020 0.004
#> GSM152817 5 0.3707 0.787568 0.000 0.000 0.312 0.000 0.680 0.008
#> GSM152818 5 0.3499 0.784299 0.000 0.000 0.320 0.000 0.680 0.000
#> GSM152819 3 0.1036 0.669749 0.000 0.004 0.964 0.000 0.024 0.008
#> GSM152820 3 0.4667 0.509924 0.000 0.028 0.732 0.000 0.108 0.132
#> GSM152821 2 0.6874 0.183013 0.000 0.420 0.364 0.008 0.072 0.136
#> GSM153115 4 0.3596 0.706407 0.000 0.232 0.000 0.748 0.004 0.016
#> GSM153116 3 0.1845 0.638176 0.000 0.004 0.916 0.000 0.072 0.008
#> GSM153117 3 0.3584 0.487187 0.000 0.244 0.740 0.000 0.004 0.012
#> GSM153118 2 0.3874 0.472633 0.000 0.636 0.356 0.000 0.000 0.008
#> GSM153119 5 0.4710 0.776467 0.000 0.012 0.312 0.000 0.632 0.044
#> GSM153120 4 0.1679 0.840532 0.000 0.012 0.000 0.936 0.016 0.036
#> GSM153121 3 0.1523 0.668838 0.000 0.008 0.940 0.000 0.044 0.008
#> GSM153122 5 0.4532 0.783581 0.000 0.008 0.292 0.000 0.656 0.044
#> GSM153123 2 0.2340 0.699535 0.000 0.852 0.148 0.000 0.000 0.000
#> GSM153124 4 0.3894 0.667503 0.000 0.268 0.000 0.708 0.004 0.020
#> GSM153125 4 0.3144 0.765318 0.000 0.172 0.000 0.808 0.004 0.016
#> GSM153126 3 0.1588 0.634839 0.000 0.000 0.924 0.000 0.072 0.004
#> GSM153127 2 0.2019 0.753569 0.000 0.900 0.000 0.088 0.000 0.012
#> GSM153128 5 0.6945 0.385851 0.000 0.044 0.168 0.020 0.432 0.336
#> GSM153129 3 0.3515 0.322800 0.000 0.324 0.676 0.000 0.000 0.000
#> GSM153130 3 0.3547 -0.000494 0.000 0.000 0.668 0.000 0.332 0.000
#> GSM153131 3 0.1890 0.667275 0.000 0.024 0.924 0.000 0.044 0.008
#> GSM153132 3 0.0551 0.674610 0.000 0.004 0.984 0.000 0.004 0.008
#> GSM153133 2 0.6655 0.183169 0.000 0.424 0.368 0.000 0.072 0.136
#> GSM153134 2 0.3864 0.203451 0.000 0.520 0.480 0.000 0.000 0.000
#> GSM153135 2 0.1806 0.753851 0.000 0.908 0.000 0.088 0.000 0.004
#> GSM153136 4 0.1296 0.845710 0.000 0.032 0.000 0.952 0.004 0.012
#> GSM153137 4 0.4867 0.538813 0.000 0.340 0.000 0.600 0.012 0.048
#> GSM153138 2 0.7561 0.140562 0.000 0.400 0.016 0.276 0.116 0.192
#> GSM153139 3 0.2278 0.570260 0.000 0.004 0.868 0.000 0.128 0.000
#> GSM153140 2 0.1753 0.755831 0.000 0.912 0.004 0.084 0.000 0.000
#> GSM153141 2 0.1806 0.753851 0.000 0.908 0.000 0.088 0.000 0.004
#> GSM153142 5 0.3647 0.751361 0.000 0.000 0.360 0.000 0.640 0.000
#> GSM153143 2 0.3364 0.735613 0.000 0.828 0.008 0.096 0.000 0.068
#> GSM153144 2 0.2340 0.699758 0.000 0.852 0.148 0.000 0.000 0.000
#> GSM153145 5 0.3482 0.786099 0.000 0.000 0.316 0.000 0.684 0.000
#> GSM153146 2 0.6874 0.183013 0.000 0.420 0.364 0.008 0.072 0.136
#> GSM153147 3 0.6546 0.144690 0.000 0.304 0.488 0.000 0.072 0.136
#> GSM153148 2 0.2056 0.756737 0.000 0.904 0.004 0.080 0.000 0.012
#> GSM153149 3 0.6658 -0.072043 0.000 0.372 0.420 0.000 0.072 0.136
#> GSM153150 4 0.1585 0.840992 0.000 0.012 0.000 0.940 0.012 0.036
#> GSM153151 3 0.7462 0.072582 0.000 0.300 0.416 0.020 0.116 0.148
#> GSM153152 3 0.4077 0.301619 0.000 0.320 0.660 0.000 0.008 0.012
#> GSM153153 2 0.4161 0.297350 0.000 0.540 0.448 0.000 0.000 0.012
#> GSM153154 3 0.0551 0.674610 0.000 0.004 0.984 0.000 0.004 0.008
#> GSM153155 2 0.6025 0.605774 0.000 0.660 0.040 0.084 0.072 0.144
#> GSM153156 3 0.4331 0.533550 0.000 0.028 0.764 0.000 0.096 0.112
#> GSM153157 5 0.4726 0.774453 0.000 0.012 0.316 0.000 0.628 0.044
#> GSM153158 3 0.1757 0.631001 0.000 0.000 0.916 0.000 0.076 0.008
#> GSM153159 5 0.3843 0.614434 0.000 0.000 0.452 0.000 0.548 0.000
#> GSM153160 3 0.2288 0.585778 0.000 0.004 0.876 0.000 0.116 0.004
#> GSM153161 2 0.1918 0.753279 0.000 0.904 0.000 0.088 0.000 0.008
#> GSM153162 3 0.3890 0.122509 0.000 0.400 0.596 0.000 0.000 0.004
#> GSM153163 3 0.2333 0.579969 0.000 0.004 0.872 0.000 0.120 0.004
#> GSM153164 2 0.4181 0.232042 0.000 0.512 0.476 0.000 0.000 0.012
#> GSM153165 3 0.2243 0.590992 0.000 0.004 0.880 0.000 0.112 0.004
#> GSM153166 3 0.4097 -0.182383 0.000 0.488 0.504 0.000 0.000 0.008
#> GSM153167 3 0.4181 -0.159402 0.000 0.476 0.512 0.000 0.000 0.012
#> GSM153168 5 0.3601 0.787678 0.000 0.000 0.312 0.000 0.684 0.004
#> GSM153169 3 0.3351 0.160357 0.000 0.000 0.712 0.000 0.288 0.000
#> GSM153170 3 0.0520 0.674097 0.000 0.008 0.984 0.000 0.008 0.000
#> GSM153171 4 0.3144 0.765318 0.000 0.172 0.000 0.808 0.004 0.016
#> GSM153172 2 0.1610 0.730247 0.000 0.916 0.084 0.000 0.000 0.000
#> GSM153173 3 0.2288 0.585778 0.000 0.004 0.876 0.000 0.116 0.004
#> GSM153174 2 0.3494 0.606582 0.000 0.736 0.252 0.000 0.000 0.012
#> GSM153175 4 0.1478 0.846292 0.000 0.032 0.000 0.944 0.004 0.020
#> GSM153176 3 0.5616 0.428814 0.000 0.012 0.684 0.104 0.084 0.116
#> GSM153177 2 0.3998 0.176829 0.000 0.504 0.492 0.000 0.000 0.004
#> GSM152931 4 0.2361 0.810972 0.000 0.104 0.000 0.880 0.004 0.012
#> GSM152932 2 0.3151 0.613944 0.000 0.748 0.252 0.000 0.000 0.000
#> GSM152933 2 0.4234 0.314625 0.000 0.544 0.440 0.000 0.000 0.016
#> GSM152934 4 0.6509 0.463974 0.000 0.044 0.008 0.524 0.176 0.248
#> GSM152935 2 0.4263 0.210791 0.000 0.504 0.480 0.000 0.000 0.016
#> GSM152936 4 0.1657 0.840731 0.000 0.012 0.000 0.936 0.012 0.040
#> GSM152937 5 0.7075 0.363717 0.000 0.044 0.180 0.024 0.412 0.340
#> GSM152938 3 0.1718 0.668615 0.000 0.016 0.932 0.000 0.044 0.008
#> GSM152939 4 0.4293 0.302190 0.000 0.448 0.000 0.536 0.004 0.012
#> GSM152940 4 0.1434 0.846641 0.000 0.028 0.000 0.948 0.012 0.012
#> GSM152941 1 0.6112 0.064635 0.476 0.032 0.000 0.404 0.024 0.064
#> GSM152942 3 0.0551 0.674822 0.000 0.008 0.984 0.000 0.004 0.004
#> GSM152943 4 0.6096 0.505411 0.000 0.028 0.004 0.552 0.160 0.256
#> GSM152944 3 0.2219 0.560038 0.000 0.000 0.864 0.000 0.136 0.000
#> GSM152945 2 0.5001 0.663791 0.000 0.740 0.016 0.084 0.060 0.100
#> GSM152946 2 0.1753 0.755831 0.000 0.912 0.004 0.084 0.000 0.000
#> GSM152947 4 0.0935 0.846865 0.000 0.032 0.000 0.964 0.004 0.000
#> GSM152948 2 0.1806 0.753851 0.000 0.908 0.000 0.088 0.000 0.004
#> GSM152949 3 0.1053 0.673449 0.000 0.004 0.964 0.000 0.020 0.012
#> GSM152950 3 0.2994 0.628440 0.000 0.020 0.856 0.000 0.096 0.028
#> GSM152951 2 0.1714 0.752607 0.000 0.908 0.000 0.092 0.000 0.000
#> GSM152952 2 0.1918 0.753279 0.000 0.904 0.000 0.088 0.000 0.008
#> GSM152953 2 0.1918 0.753279 0.000 0.904 0.000 0.088 0.000 0.008
#> GSM152954 4 0.1555 0.839400 0.000 0.008 0.000 0.940 0.012 0.040
#> GSM152955 6 0.8854 -0.149584 0.000 0.164 0.176 0.244 0.156 0.260
#> GSM152956 2 0.1918 0.753279 0.000 0.904 0.000 0.088 0.000 0.008
#> GSM152957 4 0.1757 0.837738 0.000 0.008 0.000 0.928 0.012 0.052
#> GSM152958 4 0.1194 0.846872 0.000 0.032 0.000 0.956 0.004 0.008
#> GSM152959 4 0.2015 0.829030 0.000 0.012 0.000 0.916 0.016 0.056
#> GSM152960 4 0.4278 0.717775 0.000 0.024 0.000 0.760 0.072 0.144
#> GSM152961 4 0.1307 0.846767 0.000 0.032 0.000 0.952 0.008 0.008
#> GSM152962 3 0.5692 0.447804 0.000 0.036 0.664 0.020 0.132 0.148
#> GSM152963 2 0.2019 0.753569 0.000 0.900 0.000 0.088 0.000 0.012
#> GSM152964 5 0.7138 0.372074 0.000 0.044 0.148 0.040 0.428 0.340
#> GSM152965 2 0.7411 0.117479 0.000 0.380 0.352 0.020 0.104 0.144
#> GSM152966 4 0.1296 0.845710 0.000 0.032 0.000 0.952 0.004 0.012
#> GSM152967 2 0.3074 0.750736 0.000 0.856 0.044 0.080 0.000 0.020
#> GSM152968 3 0.0665 0.675196 0.000 0.004 0.980 0.000 0.008 0.008
#> GSM152969 4 0.1296 0.845710 0.000 0.032 0.000 0.952 0.004 0.012
#> GSM152970 4 0.1820 0.836774 0.000 0.008 0.000 0.924 0.012 0.056
#> GSM152971 4 0.1296 0.845710 0.000 0.032 0.000 0.952 0.004 0.012
#> GSM152972 4 0.0935 0.847298 0.000 0.032 0.000 0.964 0.000 0.004
#> GSM152973 2 0.5309 0.356960 0.000 0.556 0.364 0.060 0.004 0.016
#> GSM152974 2 0.2562 0.684354 0.000 0.828 0.172 0.000 0.000 0.000
#> GSM152975 2 0.2491 0.691433 0.000 0.836 0.000 0.164 0.000 0.000
#> GSM152976 4 0.1642 0.846026 0.000 0.028 0.000 0.936 0.004 0.032
#> GSM152977 4 0.1577 0.838347 0.000 0.016 0.000 0.940 0.008 0.036
#> GSM152978 4 0.1679 0.840532 0.000 0.012 0.000 0.936 0.016 0.036
#> GSM152979 3 0.0767 0.672319 0.000 0.008 0.976 0.000 0.012 0.004
#> GSM152980 4 0.6900 0.466906 0.000 0.196 0.008 0.520 0.104 0.172
#> GSM152981 5 0.4610 0.773899 0.000 0.012 0.276 0.000 0.664 0.048
#> GSM152982 4 0.2658 0.814272 0.000 0.016 0.004 0.888 0.052 0.040
#> GSM152983 4 0.1296 0.845710 0.000 0.032 0.000 0.952 0.004 0.012
#> GSM152984 2 0.5844 0.482707 0.000 0.564 0.280 0.132 0.004 0.020
#> GSM152985 4 0.1605 0.836092 0.000 0.004 0.000 0.936 0.016 0.044
#> GSM152986 4 0.1296 0.845710 0.000 0.032 0.000 0.952 0.004 0.012
#> GSM152987 1 0.6105 0.169840 0.584 0.032 0.000 0.272 0.036 0.076
#> GSM152988 4 0.4249 0.365307 0.000 0.416 0.000 0.568 0.004 0.012
#> GSM152989 4 0.2698 0.799547 0.000 0.040 0.000 0.880 0.016 0.064
#> GSM152990 3 0.0767 0.672319 0.000 0.008 0.976 0.000 0.012 0.004
#> GSM152991 3 0.4238 -0.319402 0.000 0.008 0.580 0.000 0.404 0.008
#> GSM187524 6 0.5320 0.706234 0.412 0.024 0.000 0.008 0.036 0.520
#> GSM187525 6 0.5162 0.733347 0.452 0.020 0.000 0.008 0.028 0.492
#> GSM187526 6 0.5358 0.724373 0.452 0.028 0.000 0.008 0.032 0.480
#> GSM187527 4 0.4721 0.026683 0.472 0.000 0.000 0.492 0.012 0.024
#> GSM152856 1 0.0000 0.826957 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152857 1 0.4964 0.447060 0.732 0.004 0.004 0.052 0.076 0.132
#> GSM152858 6 0.3843 0.756533 0.452 0.000 0.000 0.000 0.000 0.548
#> GSM152859 6 0.5515 0.631417 0.348 0.024 0.000 0.004 0.068 0.556
#> GSM152860 6 0.3843 0.756533 0.452 0.000 0.000 0.000 0.000 0.548
#> GSM152861 1 0.1942 0.792198 0.916 0.012 0.000 0.000 0.008 0.064
#> GSM152862 6 0.3843 0.756533 0.452 0.000 0.000 0.000 0.000 0.548
#> GSM152863 1 0.1942 0.792198 0.916 0.012 0.000 0.000 0.008 0.064
#> GSM152864 1 0.1882 0.796227 0.920 0.012 0.000 0.000 0.008 0.060
#> GSM152865 1 0.1942 0.792198 0.916 0.012 0.000 0.000 0.008 0.064
#> GSM152866 1 0.0000 0.826957 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152867 1 0.1882 0.796227 0.920 0.012 0.000 0.000 0.008 0.060
#> GSM152868 1 0.1882 0.796227 0.920 0.012 0.000 0.000 0.008 0.060
#> GSM152869 1 0.1882 0.796227 0.920 0.012 0.000 0.000 0.008 0.060
#> GSM152870 6 0.3843 0.756533 0.452 0.000 0.000 0.000 0.000 0.548
#> GSM152871 6 0.3843 0.756533 0.452 0.000 0.000 0.000 0.000 0.548
#> GSM152872 6 0.3843 0.756533 0.452 0.000 0.000 0.000 0.000 0.548
#> GSM152873 1 0.0000 0.826957 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.826957 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152875 1 0.0000 0.826957 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152876 1 0.0622 0.810480 0.980 0.000 0.000 0.000 0.008 0.012
#> GSM152877 1 0.0000 0.826957 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152878 1 0.0000 0.826957 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152879 1 0.0000 0.826957 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.826957 1.000 0.000 0.000 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> ATC:kmeans 171 4.03e-27 2
#> ATC:kmeans 169 3.81e-29 3
#> ATC:kmeans 141 4.73e-27 4
#> ATC:kmeans 146 2.77e-25 5
#> ATC:kmeans 130 1.07e-24 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "skmeans"]
# you can also extract it by
# res = res_list["ATC:skmeans"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.984 0.994 0.4810 0.521 0.521
#> 3 3 0.879 0.874 0.951 0.3726 0.721 0.509
#> 4 4 0.854 0.899 0.945 0.1230 0.785 0.468
#> 5 5 0.817 0.829 0.905 0.0600 0.917 0.697
#> 6 6 0.765 0.647 0.779 0.0445 0.942 0.736
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.9927 0.000 1.000
#> GSM152805 2 0.0000 0.9927 0.000 1.000
#> GSM152806 2 0.0000 0.9927 0.000 1.000
#> GSM152807 2 0.0000 0.9927 0.000 1.000
#> GSM152808 2 0.0000 0.9927 0.000 1.000
#> GSM152809 2 0.0000 0.9927 0.000 1.000
#> GSM152810 1 0.0000 0.9954 1.000 0.000
#> GSM152811 2 0.0000 0.9927 0.000 1.000
#> GSM152812 2 0.0000 0.9927 0.000 1.000
#> GSM152813 2 0.0000 0.9927 0.000 1.000
#> GSM152814 2 0.0000 0.9927 0.000 1.000
#> GSM152815 2 0.0000 0.9927 0.000 1.000
#> GSM152816 2 0.0000 0.9927 0.000 1.000
#> GSM152817 2 0.0000 0.9927 0.000 1.000
#> GSM152818 2 0.0000 0.9927 0.000 1.000
#> GSM152819 2 0.0000 0.9927 0.000 1.000
#> GSM152820 2 0.0000 0.9927 0.000 1.000
#> GSM152821 2 0.0000 0.9927 0.000 1.000
#> GSM153115 1 0.0000 0.9954 1.000 0.000
#> GSM153116 2 0.0000 0.9927 0.000 1.000
#> GSM153117 2 0.0000 0.9927 0.000 1.000
#> GSM153118 2 0.0000 0.9927 0.000 1.000
#> GSM153119 2 0.0000 0.9927 0.000 1.000
#> GSM153120 1 0.0000 0.9954 1.000 0.000
#> GSM153121 2 0.0000 0.9927 0.000 1.000
#> GSM153122 2 0.0000 0.9927 0.000 1.000
#> GSM153123 2 0.0000 0.9927 0.000 1.000
#> GSM153124 2 0.0672 0.9849 0.008 0.992
#> GSM153125 1 0.0000 0.9954 1.000 0.000
#> GSM153126 2 0.0000 0.9927 0.000 1.000
#> GSM153127 2 0.0000 0.9927 0.000 1.000
#> GSM153128 2 0.0000 0.9927 0.000 1.000
#> GSM153129 2 0.0000 0.9927 0.000 1.000
#> GSM153130 2 0.0000 0.9927 0.000 1.000
#> GSM153131 2 0.0000 0.9927 0.000 1.000
#> GSM153132 2 0.0000 0.9927 0.000 1.000
#> GSM153133 2 0.0000 0.9927 0.000 1.000
#> GSM153134 2 0.0000 0.9927 0.000 1.000
#> GSM153135 2 0.0000 0.9927 0.000 1.000
#> GSM153136 1 0.0000 0.9954 1.000 0.000
#> GSM153137 1 0.0000 0.9954 1.000 0.000
#> GSM153138 2 0.0000 0.9927 0.000 1.000
#> GSM153139 2 0.0000 0.9927 0.000 1.000
#> GSM153140 2 0.0000 0.9927 0.000 1.000
#> GSM153141 2 0.0000 0.9927 0.000 1.000
#> GSM153142 2 0.0000 0.9927 0.000 1.000
#> GSM153143 2 0.0000 0.9927 0.000 1.000
#> GSM153144 2 0.0000 0.9927 0.000 1.000
#> GSM153145 2 0.0000 0.9927 0.000 1.000
#> GSM153146 2 0.0000 0.9927 0.000 1.000
#> GSM153147 2 0.0000 0.9927 0.000 1.000
#> GSM153148 2 0.0000 0.9927 0.000 1.000
#> GSM153149 2 0.0000 0.9927 0.000 1.000
#> GSM153150 1 0.0000 0.9954 1.000 0.000
#> GSM153151 2 0.0000 0.9927 0.000 1.000
#> GSM153152 2 0.0000 0.9927 0.000 1.000
#> GSM153153 2 0.0000 0.9927 0.000 1.000
#> GSM153154 2 0.0000 0.9927 0.000 1.000
#> GSM153155 2 0.0000 0.9927 0.000 1.000
#> GSM153156 2 0.0000 0.9927 0.000 1.000
#> GSM153157 2 0.0000 0.9927 0.000 1.000
#> GSM153158 2 0.0000 0.9927 0.000 1.000
#> GSM153159 2 0.0000 0.9927 0.000 1.000
#> GSM153160 2 0.0000 0.9927 0.000 1.000
#> GSM153161 2 0.0000 0.9927 0.000 1.000
#> GSM153162 2 0.0000 0.9927 0.000 1.000
#> GSM153163 2 0.0000 0.9927 0.000 1.000
#> GSM153164 2 0.0000 0.9927 0.000 1.000
#> GSM153165 2 0.0000 0.9927 0.000 1.000
#> GSM153166 2 0.0000 0.9927 0.000 1.000
#> GSM153167 2 0.0000 0.9927 0.000 1.000
#> GSM153168 2 0.0000 0.9927 0.000 1.000
#> GSM153169 2 0.0000 0.9927 0.000 1.000
#> GSM153170 2 0.0000 0.9927 0.000 1.000
#> GSM153171 1 0.0000 0.9954 1.000 0.000
#> GSM153172 2 0.0000 0.9927 0.000 1.000
#> GSM153173 2 0.0000 0.9927 0.000 1.000
#> GSM153174 2 0.0000 0.9927 0.000 1.000
#> GSM153175 1 0.0000 0.9954 1.000 0.000
#> GSM153176 2 0.9993 0.0613 0.484 0.516
#> GSM153177 2 0.0000 0.9927 0.000 1.000
#> GSM152931 1 0.0000 0.9954 1.000 0.000
#> GSM152932 2 0.0000 0.9927 0.000 1.000
#> GSM152933 2 0.0000 0.9927 0.000 1.000
#> GSM152934 1 0.0000 0.9954 1.000 0.000
#> GSM152935 2 0.0000 0.9927 0.000 1.000
#> GSM152936 1 0.0000 0.9954 1.000 0.000
#> GSM152937 2 0.0000 0.9927 0.000 1.000
#> GSM152938 2 0.0000 0.9927 0.000 1.000
#> GSM152939 1 0.6247 0.8164 0.844 0.156
#> GSM152940 1 0.0000 0.9954 1.000 0.000
#> GSM152941 1 0.0000 0.9954 1.000 0.000
#> GSM152942 2 0.0000 0.9927 0.000 1.000
#> GSM152943 1 0.0000 0.9954 1.000 0.000
#> GSM152944 2 0.0000 0.9927 0.000 1.000
#> GSM152945 2 0.0000 0.9927 0.000 1.000
#> GSM152946 2 0.0000 0.9927 0.000 1.000
#> GSM152947 1 0.0000 0.9954 1.000 0.000
#> GSM152948 2 0.0000 0.9927 0.000 1.000
#> GSM152949 2 0.0000 0.9927 0.000 1.000
#> GSM152950 2 0.0000 0.9927 0.000 1.000
#> GSM152951 2 0.0000 0.9927 0.000 1.000
#> GSM152952 2 0.0000 0.9927 0.000 1.000
#> GSM152953 2 0.0000 0.9927 0.000 1.000
#> GSM152954 1 0.0000 0.9954 1.000 0.000
#> GSM152955 2 0.0000 0.9927 0.000 1.000
#> GSM152956 2 0.0000 0.9927 0.000 1.000
#> GSM152957 1 0.0000 0.9954 1.000 0.000
#> GSM152958 1 0.0000 0.9954 1.000 0.000
#> GSM152959 1 0.0000 0.9954 1.000 0.000
#> GSM152960 1 0.0000 0.9954 1.000 0.000
#> GSM152961 1 0.0000 0.9954 1.000 0.000
#> GSM152962 2 0.0000 0.9927 0.000 1.000
#> GSM152963 2 0.0000 0.9927 0.000 1.000
#> GSM152964 1 0.0000 0.9954 1.000 0.000
#> GSM152965 2 0.0000 0.9927 0.000 1.000
#> GSM152966 1 0.0000 0.9954 1.000 0.000
#> GSM152967 2 0.0000 0.9927 0.000 1.000
#> GSM152968 2 0.0000 0.9927 0.000 1.000
#> GSM152969 1 0.0000 0.9954 1.000 0.000
#> GSM152970 1 0.0000 0.9954 1.000 0.000
#> GSM152971 1 0.0000 0.9954 1.000 0.000
#> GSM152972 1 0.0000 0.9954 1.000 0.000
#> GSM152973 2 0.0000 0.9927 0.000 1.000
#> GSM152974 2 0.0000 0.9927 0.000 1.000
#> GSM152975 2 0.0000 0.9927 0.000 1.000
#> GSM152976 1 0.0000 0.9954 1.000 0.000
#> GSM152977 1 0.0000 0.9954 1.000 0.000
#> GSM152978 1 0.0000 0.9954 1.000 0.000
#> GSM152979 2 0.0000 0.9927 0.000 1.000
#> GSM152980 2 0.8144 0.6613 0.252 0.748
#> GSM152981 2 0.0000 0.9927 0.000 1.000
#> GSM152982 1 0.0000 0.9954 1.000 0.000
#> GSM152983 1 0.5946 0.8320 0.856 0.144
#> GSM152984 2 0.0000 0.9927 0.000 1.000
#> GSM152985 1 0.0000 0.9954 1.000 0.000
#> GSM152986 1 0.0000 0.9954 1.000 0.000
#> GSM152987 1 0.0000 0.9954 1.000 0.000
#> GSM152988 2 0.0000 0.9927 0.000 1.000
#> GSM152989 1 0.0000 0.9954 1.000 0.000
#> GSM152990 2 0.0000 0.9927 0.000 1.000
#> GSM152991 2 0.0000 0.9927 0.000 1.000
#> GSM187524 1 0.0000 0.9954 1.000 0.000
#> GSM187525 1 0.0000 0.9954 1.000 0.000
#> GSM187526 1 0.0000 0.9954 1.000 0.000
#> GSM187527 1 0.0000 0.9954 1.000 0.000
#> GSM152856 1 0.0000 0.9954 1.000 0.000
#> GSM152857 1 0.0000 0.9954 1.000 0.000
#> GSM152858 1 0.0000 0.9954 1.000 0.000
#> GSM152859 1 0.0000 0.9954 1.000 0.000
#> GSM152860 1 0.0000 0.9954 1.000 0.000
#> GSM152861 1 0.0000 0.9954 1.000 0.000
#> GSM152862 1 0.0000 0.9954 1.000 0.000
#> GSM152863 1 0.0000 0.9954 1.000 0.000
#> GSM152864 1 0.0000 0.9954 1.000 0.000
#> GSM152865 1 0.0000 0.9954 1.000 0.000
#> GSM152866 1 0.0000 0.9954 1.000 0.000
#> GSM152867 1 0.0000 0.9954 1.000 0.000
#> GSM152868 1 0.0000 0.9954 1.000 0.000
#> GSM152869 1 0.0000 0.9954 1.000 0.000
#> GSM152870 1 0.0000 0.9954 1.000 0.000
#> GSM152871 1 0.0000 0.9954 1.000 0.000
#> GSM152872 1 0.0000 0.9954 1.000 0.000
#> GSM152873 1 0.0000 0.9954 1.000 0.000
#> GSM152874 1 0.0000 0.9954 1.000 0.000
#> GSM152875 1 0.0000 0.9954 1.000 0.000
#> GSM152876 1 0.0000 0.9954 1.000 0.000
#> GSM152877 1 0.0000 0.9954 1.000 0.000
#> GSM152878 1 0.0000 0.9954 1.000 0.000
#> GSM152879 1 0.0000 0.9954 1.000 0.000
#> GSM152880 1 0.0000 0.9954 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152805 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152806 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152807 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152808 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152809 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152810 1 0.4750 0.6975 0.784 0.000 0.216
#> GSM152811 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152812 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152813 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152814 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152815 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152816 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152817 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152818 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152819 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152820 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152821 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153115 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153116 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153117 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153118 3 0.4346 0.7683 0.000 0.184 0.816
#> GSM153119 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153120 1 0.6225 0.1562 0.568 0.432 0.000
#> GSM153121 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153122 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153123 2 0.0237 0.9059 0.000 0.996 0.004
#> GSM153124 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153125 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153126 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153127 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153128 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153129 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153130 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153131 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153132 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153133 3 0.0237 0.9791 0.000 0.004 0.996
#> GSM153134 3 0.2066 0.9248 0.000 0.060 0.940
#> GSM153135 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153136 2 0.0237 0.9065 0.004 0.996 0.000
#> GSM153137 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153138 2 0.3412 0.8023 0.000 0.876 0.124
#> GSM153139 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153140 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153141 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153142 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153143 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153144 2 0.0237 0.9059 0.000 0.996 0.004
#> GSM153145 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153146 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153147 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153148 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153149 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153150 2 0.6305 0.1260 0.484 0.516 0.000
#> GSM153151 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153152 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153153 3 0.0592 0.9730 0.000 0.012 0.988
#> GSM153154 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153155 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153156 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153157 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153158 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153159 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153160 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153161 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153162 3 0.0424 0.9762 0.000 0.008 0.992
#> GSM153163 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153164 3 0.0424 0.9762 0.000 0.008 0.992
#> GSM153165 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153166 3 0.0592 0.9730 0.000 0.012 0.988
#> GSM153167 3 0.0424 0.9762 0.000 0.008 0.992
#> GSM153168 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153169 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153170 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153171 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153172 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM153173 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM153174 3 0.6299 0.1323 0.000 0.476 0.524
#> GSM153175 2 0.5216 0.6432 0.260 0.740 0.000
#> GSM153176 3 0.0592 0.9709 0.012 0.000 0.988
#> GSM153177 3 0.0592 0.9730 0.000 0.012 0.988
#> GSM152931 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152932 3 0.6062 0.3842 0.000 0.384 0.616
#> GSM152933 3 0.0592 0.9730 0.000 0.012 0.988
#> GSM152934 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152935 3 0.0237 0.9791 0.000 0.004 0.996
#> GSM152936 2 0.6026 0.4296 0.376 0.624 0.000
#> GSM152937 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152938 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152939 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152940 2 0.6299 0.1533 0.476 0.524 0.000
#> GSM152941 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152942 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152943 1 0.5706 0.4651 0.680 0.320 0.000
#> GSM152944 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152945 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152946 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152947 1 0.6307 -0.0572 0.512 0.488 0.000
#> GSM152948 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152949 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152950 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152951 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152952 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152953 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152954 1 0.6235 0.1426 0.564 0.436 0.000
#> GSM152955 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152956 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152957 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152958 2 0.6111 0.3825 0.396 0.604 0.000
#> GSM152959 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152960 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152961 2 0.6307 0.1121 0.488 0.512 0.000
#> GSM152962 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152963 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152964 1 0.5621 0.5391 0.692 0.000 0.308
#> GSM152965 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152966 2 0.3340 0.8127 0.120 0.880 0.000
#> GSM152967 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152968 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152969 2 0.5621 0.5656 0.308 0.692 0.000
#> GSM152970 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152971 2 0.0424 0.9039 0.008 0.992 0.000
#> GSM152972 2 0.5733 0.5366 0.324 0.676 0.000
#> GSM152973 2 0.4702 0.6830 0.000 0.788 0.212
#> GSM152974 2 0.3116 0.8172 0.000 0.892 0.108
#> GSM152975 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152976 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152977 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152978 2 0.6225 0.2885 0.432 0.568 0.000
#> GSM152979 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152980 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152981 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152982 1 0.9579 0.0475 0.432 0.368 0.200
#> GSM152983 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152984 2 0.2959 0.8158 0.000 0.900 0.100
#> GSM152985 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152986 2 0.3941 0.7757 0.156 0.844 0.000
#> GSM152987 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152988 2 0.0000 0.9088 0.000 1.000 0.000
#> GSM152989 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152990 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM152991 3 0.0000 0.9818 0.000 0.000 1.000
#> GSM187524 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM187525 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM187526 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM187527 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152856 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152857 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152858 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152859 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152860 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152861 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152862 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152863 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152864 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152866 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152867 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152870 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152871 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152873 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152874 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152875 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152876 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152877 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152878 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152879 1 0.0000 0.9322 1.000 0.000 0.000
#> GSM152880 1 0.0000 0.9322 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.0817 0.887 0.000 0.976 0.000 0.024
#> GSM152805 3 0.0469 0.975 0.000 0.012 0.988 0.000
#> GSM152806 3 0.0000 0.975 0.000 0.000 1.000 0.000
#> GSM152807 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM152808 3 0.0000 0.975 0.000 0.000 1.000 0.000
#> GSM152809 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM152810 3 0.4012 0.721 0.204 0.004 0.788 0.004
#> GSM152811 3 0.0188 0.974 0.000 0.004 0.996 0.000
#> GSM152812 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM152813 2 0.0817 0.887 0.000 0.976 0.000 0.024
#> GSM152814 2 0.0592 0.887 0.000 0.984 0.000 0.016
#> GSM152815 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM152816 3 0.0817 0.973 0.000 0.024 0.976 0.000
#> GSM152817 3 0.0000 0.975 0.000 0.000 1.000 0.000
#> GSM152818 3 0.0000 0.975 0.000 0.000 1.000 0.000
#> GSM152819 3 0.0707 0.974 0.000 0.020 0.980 0.000
#> GSM152820 3 0.0376 0.972 0.000 0.004 0.992 0.004
#> GSM152821 2 0.3831 0.793 0.000 0.792 0.204 0.004
#> GSM153115 4 0.0592 0.923 0.000 0.016 0.000 0.984
#> GSM153116 3 0.0707 0.974 0.000 0.020 0.980 0.000
#> GSM153117 2 0.4406 0.662 0.000 0.700 0.300 0.000
#> GSM153118 2 0.2647 0.850 0.000 0.880 0.120 0.000
#> GSM153119 3 0.0188 0.974 0.000 0.004 0.996 0.000
#> GSM153120 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM153121 3 0.0592 0.975 0.000 0.016 0.984 0.000
#> GSM153122 3 0.0000 0.975 0.000 0.000 1.000 0.000
#> GSM153123 2 0.0188 0.885 0.000 0.996 0.000 0.004
#> GSM153124 4 0.2814 0.845 0.000 0.132 0.000 0.868
#> GSM153125 4 0.0592 0.923 0.000 0.016 0.000 0.984
#> GSM153126 3 0.0188 0.975 0.000 0.004 0.996 0.000
#> GSM153127 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM153128 3 0.0376 0.972 0.000 0.004 0.992 0.004
#> GSM153129 2 0.4790 0.505 0.000 0.620 0.380 0.000
#> GSM153130 3 0.0469 0.975 0.000 0.012 0.988 0.000
#> GSM153131 3 0.0817 0.973 0.000 0.024 0.976 0.000
#> GSM153132 3 0.0707 0.974 0.000 0.020 0.980 0.000
#> GSM153133 2 0.3355 0.831 0.000 0.836 0.160 0.004
#> GSM153134 2 0.3123 0.834 0.000 0.844 0.156 0.000
#> GSM153135 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM153136 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM153137 4 0.4134 0.667 0.000 0.260 0.000 0.740
#> GSM153138 2 0.2334 0.846 0.000 0.908 0.004 0.088
#> GSM153139 3 0.0817 0.973 0.000 0.024 0.976 0.000
#> GSM153140 2 0.0817 0.887 0.000 0.976 0.000 0.024
#> GSM153141 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM153142 3 0.0000 0.975 0.000 0.000 1.000 0.000
#> GSM153143 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM153144 2 0.0188 0.885 0.000 0.996 0.000 0.004
#> GSM153145 3 0.0000 0.975 0.000 0.000 1.000 0.000
#> GSM153146 2 0.3751 0.802 0.000 0.800 0.196 0.004
#> GSM153147 3 0.3908 0.706 0.000 0.212 0.784 0.004
#> GSM153148 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM153149 2 0.4677 0.635 0.000 0.680 0.316 0.004
#> GSM153150 4 0.0000 0.926 0.000 0.000 0.000 1.000
#> GSM153151 3 0.0524 0.971 0.000 0.008 0.988 0.004
#> GSM153152 2 0.4713 0.555 0.000 0.640 0.360 0.000
#> GSM153153 2 0.3123 0.834 0.000 0.844 0.156 0.000
#> GSM153154 3 0.0707 0.974 0.000 0.020 0.980 0.000
#> GSM153155 2 0.1211 0.881 0.000 0.960 0.000 0.040
#> GSM153156 3 0.0188 0.974 0.000 0.004 0.996 0.000
#> GSM153157 3 0.0188 0.974 0.000 0.004 0.996 0.000
#> GSM153158 3 0.0707 0.974 0.000 0.020 0.980 0.000
#> GSM153159 3 0.0000 0.975 0.000 0.000 1.000 0.000
#> GSM153160 3 0.0817 0.973 0.000 0.024 0.976 0.000
#> GSM153161 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM153162 2 0.3123 0.834 0.000 0.844 0.156 0.000
#> GSM153163 3 0.0817 0.973 0.000 0.024 0.976 0.000
#> GSM153164 2 0.3123 0.834 0.000 0.844 0.156 0.000
#> GSM153165 3 0.0817 0.973 0.000 0.024 0.976 0.000
#> GSM153166 2 0.3123 0.834 0.000 0.844 0.156 0.000
#> GSM153167 2 0.3024 0.838 0.000 0.852 0.148 0.000
#> GSM153168 3 0.0000 0.975 0.000 0.000 1.000 0.000
#> GSM153169 3 0.0000 0.975 0.000 0.000 1.000 0.000
#> GSM153170 3 0.0817 0.973 0.000 0.024 0.976 0.000
#> GSM153171 4 0.0336 0.926 0.000 0.008 0.000 0.992
#> GSM153172 2 0.0188 0.885 0.000 0.996 0.000 0.004
#> GSM153173 3 0.0817 0.973 0.000 0.024 0.976 0.000
#> GSM153174 2 0.0336 0.884 0.000 0.992 0.008 0.000
#> GSM153175 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM153176 3 0.1452 0.945 0.036 0.008 0.956 0.000
#> GSM153177 2 0.3123 0.834 0.000 0.844 0.156 0.000
#> GSM152931 4 0.0336 0.926 0.000 0.008 0.000 0.992
#> GSM152932 2 0.0469 0.883 0.000 0.988 0.012 0.000
#> GSM152933 2 0.3123 0.834 0.000 0.844 0.156 0.000
#> GSM152934 4 0.5262 0.545 0.304 0.004 0.020 0.672
#> GSM152935 2 0.3266 0.826 0.000 0.832 0.168 0.000
#> GSM152936 4 0.0000 0.926 0.000 0.000 0.000 1.000
#> GSM152937 3 0.0376 0.972 0.000 0.004 0.992 0.004
#> GSM152938 3 0.0817 0.973 0.000 0.024 0.976 0.000
#> GSM152939 4 0.1637 0.899 0.000 0.060 0.000 0.940
#> GSM152940 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM152941 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152942 3 0.0817 0.973 0.000 0.024 0.976 0.000
#> GSM152943 4 0.3289 0.832 0.120 0.004 0.012 0.864
#> GSM152944 3 0.0707 0.974 0.000 0.020 0.980 0.000
#> GSM152945 2 0.1004 0.886 0.000 0.972 0.004 0.024
#> GSM152946 2 0.0817 0.887 0.000 0.976 0.000 0.024
#> GSM152947 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM152948 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM152949 3 0.0707 0.974 0.000 0.020 0.980 0.000
#> GSM152950 3 0.0469 0.975 0.000 0.012 0.988 0.000
#> GSM152951 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM152952 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM152953 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM152954 4 0.0188 0.925 0.004 0.000 0.000 0.996
#> GSM152955 3 0.0524 0.970 0.000 0.004 0.988 0.008
#> GSM152956 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM152957 1 0.3610 0.738 0.800 0.000 0.000 0.200
#> GSM152958 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM152959 1 0.4843 0.316 0.604 0.000 0.000 0.396
#> GSM152960 4 0.3306 0.799 0.156 0.004 0.000 0.840
#> GSM152961 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM152962 3 0.0376 0.972 0.000 0.004 0.992 0.004
#> GSM152963 2 0.0921 0.887 0.000 0.972 0.000 0.028
#> GSM152964 3 0.3631 0.773 0.168 0.004 0.824 0.004
#> GSM152965 2 0.4122 0.764 0.000 0.760 0.236 0.004
#> GSM152966 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM152967 2 0.0817 0.887 0.000 0.976 0.000 0.024
#> GSM152968 3 0.0707 0.974 0.000 0.020 0.980 0.000
#> GSM152969 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM152970 1 0.3649 0.733 0.796 0.000 0.000 0.204
#> GSM152971 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM152972 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM152973 2 0.5203 0.660 0.000 0.720 0.232 0.048
#> GSM152974 2 0.0188 0.885 0.000 0.996 0.000 0.004
#> GSM152975 2 0.3942 0.645 0.000 0.764 0.000 0.236
#> GSM152976 4 0.1867 0.882 0.072 0.000 0.000 0.928
#> GSM152977 4 0.2081 0.872 0.084 0.000 0.000 0.916
#> GSM152978 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM152979 3 0.0817 0.973 0.000 0.024 0.976 0.000
#> GSM152980 4 0.4543 0.567 0.000 0.324 0.000 0.676
#> GSM152981 3 0.0188 0.974 0.000 0.004 0.996 0.000
#> GSM152982 4 0.0779 0.913 0.000 0.004 0.016 0.980
#> GSM152983 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM152984 4 0.5292 0.201 0.000 0.480 0.008 0.512
#> GSM152985 4 0.3123 0.802 0.156 0.000 0.000 0.844
#> GSM152986 4 0.0188 0.927 0.000 0.004 0.000 0.996
#> GSM152987 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152988 4 0.1792 0.894 0.000 0.068 0.000 0.932
#> GSM152989 1 0.0188 0.971 0.996 0.000 0.000 0.004
#> GSM152990 3 0.0817 0.973 0.000 0.024 0.976 0.000
#> GSM152991 3 0.0188 0.974 0.000 0.004 0.996 0.000
#> GSM187524 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM187525 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM187526 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM187527 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152856 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152857 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152858 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152859 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152860 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152861 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152862 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152863 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152864 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152866 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152867 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152868 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152870 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152871 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152872 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152873 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152875 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152876 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152877 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152878 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152879 1 0.0000 0.975 1.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.975 1.000 0.000 0.000 0.000
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.0000 0.832 0.000 1.000 0.000 0.000 0.000
#> GSM152805 3 0.1197 0.907 0.000 0.000 0.952 0.000 0.048
#> GSM152806 3 0.1732 0.900 0.000 0.000 0.920 0.000 0.080
#> GSM152807 2 0.0162 0.831 0.000 0.996 0.000 0.000 0.004
#> GSM152808 3 0.1908 0.896 0.000 0.000 0.908 0.000 0.092
#> GSM152809 2 0.0290 0.831 0.000 0.992 0.000 0.000 0.008
#> GSM152810 5 0.2929 0.738 0.008 0.000 0.152 0.000 0.840
#> GSM152811 3 0.1965 0.894 0.000 0.000 0.904 0.000 0.096
#> GSM152812 2 0.0703 0.828 0.000 0.976 0.000 0.000 0.024
#> GSM152813 2 0.0000 0.832 0.000 1.000 0.000 0.000 0.000
#> GSM152814 2 0.0000 0.832 0.000 1.000 0.000 0.000 0.000
#> GSM152815 2 0.0162 0.831 0.000 0.996 0.000 0.000 0.004
#> GSM152816 3 0.0404 0.912 0.000 0.000 0.988 0.000 0.012
#> GSM152817 3 0.1908 0.896 0.000 0.000 0.908 0.000 0.092
#> GSM152818 3 0.1671 0.901 0.000 0.000 0.924 0.000 0.076
#> GSM152819 3 0.0794 0.905 0.000 0.000 0.972 0.000 0.028
#> GSM152820 3 0.4273 0.161 0.000 0.000 0.552 0.000 0.448
#> GSM152821 5 0.5680 0.645 0.000 0.160 0.212 0.000 0.628
#> GSM153115 4 0.1704 0.891 0.000 0.068 0.000 0.928 0.004
#> GSM153116 3 0.1043 0.901 0.000 0.000 0.960 0.000 0.040
#> GSM153117 3 0.3759 0.683 0.000 0.136 0.808 0.000 0.056
#> GSM153118 2 0.4190 0.696 0.000 0.768 0.172 0.000 0.060
#> GSM153119 3 0.1965 0.894 0.000 0.000 0.904 0.000 0.096
#> GSM153120 4 0.1671 0.899 0.000 0.000 0.000 0.924 0.076
#> GSM153121 3 0.0162 0.912 0.000 0.000 0.996 0.000 0.004
#> GSM153122 3 0.1908 0.896 0.000 0.000 0.908 0.000 0.092
#> GSM153123 2 0.1012 0.829 0.000 0.968 0.012 0.000 0.020
#> GSM153124 4 0.3430 0.718 0.000 0.220 0.000 0.776 0.004
#> GSM153125 4 0.1638 0.894 0.000 0.064 0.000 0.932 0.004
#> GSM153126 3 0.1121 0.910 0.000 0.000 0.956 0.000 0.044
#> GSM153127 2 0.1197 0.827 0.000 0.952 0.000 0.000 0.048
#> GSM153128 5 0.2852 0.727 0.000 0.000 0.172 0.000 0.828
#> GSM153129 3 0.4602 0.502 0.000 0.240 0.708 0.000 0.052
#> GSM153130 3 0.1043 0.909 0.000 0.000 0.960 0.000 0.040
#> GSM153131 3 0.0162 0.911 0.000 0.000 0.996 0.000 0.004
#> GSM153132 3 0.1043 0.897 0.000 0.000 0.960 0.000 0.040
#> GSM153133 5 0.5583 0.650 0.000 0.152 0.208 0.000 0.640
#> GSM153134 2 0.4522 0.637 0.000 0.708 0.248 0.000 0.044
#> GSM153135 2 0.0963 0.830 0.000 0.964 0.000 0.000 0.036
#> GSM153136 4 0.0000 0.924 0.000 0.000 0.000 1.000 0.000
#> GSM153137 2 0.6343 0.156 0.000 0.492 0.000 0.332 0.176
#> GSM153138 5 0.3055 0.676 0.000 0.144 0.000 0.016 0.840
#> GSM153139 3 0.0000 0.912 0.000 0.000 1.000 0.000 0.000
#> GSM153140 2 0.0000 0.832 0.000 1.000 0.000 0.000 0.000
#> GSM153141 2 0.0510 0.830 0.000 0.984 0.000 0.000 0.016
#> GSM153142 3 0.1908 0.896 0.000 0.000 0.908 0.000 0.092
#> GSM153143 2 0.3586 0.580 0.000 0.736 0.000 0.000 0.264
#> GSM153144 2 0.1648 0.822 0.000 0.940 0.020 0.000 0.040
#> GSM153145 3 0.1908 0.896 0.000 0.000 0.908 0.000 0.092
#> GSM153146 5 0.5590 0.652 0.000 0.156 0.204 0.000 0.640
#> GSM153147 5 0.4820 0.608 0.000 0.036 0.332 0.000 0.632
#> GSM153148 2 0.1197 0.827 0.000 0.952 0.000 0.000 0.048
#> GSM153149 5 0.5284 0.678 0.000 0.104 0.236 0.000 0.660
#> GSM153150 4 0.1671 0.899 0.000 0.000 0.000 0.924 0.076
#> GSM153151 5 0.3074 0.725 0.000 0.000 0.196 0.000 0.804
#> GSM153152 3 0.3464 0.749 0.000 0.096 0.836 0.000 0.068
#> GSM153153 2 0.4497 0.660 0.000 0.732 0.208 0.000 0.060
#> GSM153154 3 0.1121 0.898 0.000 0.000 0.956 0.000 0.044
#> GSM153155 5 0.3816 0.497 0.000 0.304 0.000 0.000 0.696
#> GSM153156 3 0.2516 0.857 0.000 0.000 0.860 0.000 0.140
#> GSM153157 3 0.1965 0.894 0.000 0.000 0.904 0.000 0.096
#> GSM153158 3 0.0963 0.904 0.000 0.000 0.964 0.000 0.036
#> GSM153159 3 0.1908 0.896 0.000 0.000 0.908 0.000 0.092
#> GSM153160 3 0.0000 0.912 0.000 0.000 1.000 0.000 0.000
#> GSM153161 2 0.0794 0.827 0.000 0.972 0.000 0.000 0.028
#> GSM153162 2 0.4969 0.566 0.000 0.652 0.292 0.000 0.056
#> GSM153163 3 0.0000 0.912 0.000 0.000 1.000 0.000 0.000
#> GSM153164 2 0.4666 0.634 0.000 0.704 0.240 0.000 0.056
#> GSM153165 3 0.0000 0.912 0.000 0.000 1.000 0.000 0.000
#> GSM153166 2 0.4693 0.630 0.000 0.700 0.244 0.000 0.056
#> GSM153167 2 0.4949 0.573 0.000 0.656 0.288 0.000 0.056
#> GSM153168 3 0.1908 0.896 0.000 0.000 0.908 0.000 0.092
#> GSM153169 3 0.1341 0.905 0.000 0.000 0.944 0.000 0.056
#> GSM153170 3 0.1124 0.889 0.000 0.004 0.960 0.000 0.036
#> GSM153171 4 0.1638 0.894 0.000 0.064 0.000 0.932 0.004
#> GSM153172 2 0.0880 0.829 0.000 0.968 0.000 0.000 0.032
#> GSM153173 3 0.0000 0.912 0.000 0.000 1.000 0.000 0.000
#> GSM153174 2 0.2446 0.803 0.000 0.900 0.044 0.000 0.056
#> GSM153175 4 0.0162 0.923 0.000 0.000 0.000 0.996 0.004
#> GSM153176 3 0.3475 0.735 0.012 0.000 0.804 0.004 0.180
#> GSM153177 2 0.4719 0.626 0.000 0.696 0.248 0.000 0.056
#> GSM152931 4 0.0671 0.918 0.000 0.016 0.000 0.980 0.004
#> GSM152932 2 0.2504 0.801 0.000 0.896 0.064 0.000 0.040
#> GSM152933 2 0.4558 0.659 0.000 0.728 0.208 0.000 0.064
#> GSM152934 5 0.2824 0.681 0.032 0.000 0.000 0.096 0.872
#> GSM152935 2 0.4898 0.615 0.000 0.684 0.248 0.000 0.068
#> GSM152936 4 0.1732 0.897 0.000 0.000 0.000 0.920 0.080
#> GSM152937 5 0.2605 0.743 0.000 0.000 0.148 0.000 0.852
#> GSM152938 3 0.0000 0.912 0.000 0.000 1.000 0.000 0.000
#> GSM152939 4 0.1768 0.888 0.000 0.072 0.000 0.924 0.004
#> GSM152940 4 0.0510 0.923 0.000 0.000 0.000 0.984 0.016
#> GSM152941 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152942 3 0.0000 0.912 0.000 0.000 1.000 0.000 0.000
#> GSM152943 5 0.2674 0.667 0.012 0.000 0.000 0.120 0.868
#> GSM152944 3 0.0000 0.912 0.000 0.000 1.000 0.000 0.000
#> GSM152945 2 0.4192 0.225 0.000 0.596 0.000 0.000 0.404
#> GSM152946 2 0.0000 0.832 0.000 1.000 0.000 0.000 0.000
#> GSM152947 4 0.0290 0.924 0.000 0.000 0.000 0.992 0.008
#> GSM152948 2 0.0162 0.831 0.000 0.996 0.000 0.000 0.004
#> GSM152949 3 0.0963 0.897 0.000 0.000 0.964 0.000 0.036
#> GSM152950 3 0.1478 0.899 0.000 0.000 0.936 0.000 0.064
#> GSM152951 2 0.0162 0.831 0.000 0.996 0.000 0.000 0.004
#> GSM152952 2 0.0794 0.827 0.000 0.972 0.000 0.000 0.028
#> GSM152953 2 0.0963 0.828 0.000 0.964 0.000 0.000 0.036
#> GSM152954 4 0.1671 0.899 0.000 0.000 0.000 0.924 0.076
#> GSM152955 5 0.2074 0.752 0.000 0.000 0.104 0.000 0.896
#> GSM152956 2 0.0794 0.827 0.000 0.972 0.000 0.000 0.028
#> GSM152957 1 0.3146 0.821 0.844 0.000 0.000 0.128 0.028
#> GSM152958 4 0.0290 0.924 0.000 0.000 0.000 0.992 0.008
#> GSM152959 1 0.5037 0.602 0.684 0.000 0.000 0.228 0.088
#> GSM152960 5 0.3151 0.639 0.020 0.000 0.000 0.144 0.836
#> GSM152961 4 0.0162 0.924 0.000 0.000 0.000 0.996 0.004
#> GSM152962 5 0.3932 0.563 0.000 0.000 0.328 0.000 0.672
#> GSM152963 2 0.1197 0.827 0.000 0.952 0.000 0.000 0.048
#> GSM152964 5 0.3055 0.741 0.016 0.000 0.144 0.000 0.840
#> GSM152965 5 0.4747 0.712 0.000 0.084 0.196 0.000 0.720
#> GSM152966 4 0.0000 0.924 0.000 0.000 0.000 1.000 0.000
#> GSM152967 2 0.1956 0.819 0.000 0.916 0.008 0.000 0.076
#> GSM152968 3 0.1121 0.898 0.000 0.000 0.956 0.000 0.044
#> GSM152969 4 0.0290 0.924 0.000 0.000 0.000 0.992 0.008
#> GSM152970 1 0.3687 0.751 0.792 0.000 0.000 0.180 0.028
#> GSM152971 4 0.0000 0.924 0.000 0.000 0.000 1.000 0.000
#> GSM152972 4 0.0404 0.923 0.000 0.000 0.000 0.988 0.012
#> GSM152973 2 0.6297 0.280 0.000 0.512 0.360 0.116 0.012
#> GSM152974 2 0.1668 0.821 0.000 0.940 0.028 0.000 0.032
#> GSM152975 2 0.3177 0.636 0.000 0.792 0.000 0.208 0.000
#> GSM152976 4 0.0671 0.917 0.016 0.000 0.000 0.980 0.004
#> GSM152977 4 0.2505 0.879 0.020 0.000 0.000 0.888 0.092
#> GSM152978 4 0.1671 0.899 0.000 0.000 0.000 0.924 0.076
#> GSM152979 3 0.0000 0.912 0.000 0.000 1.000 0.000 0.000
#> GSM152980 5 0.3359 0.680 0.000 0.072 0.000 0.084 0.844
#> GSM152981 3 0.2230 0.880 0.000 0.000 0.884 0.000 0.116
#> GSM152982 4 0.2648 0.840 0.000 0.000 0.000 0.848 0.152
#> GSM152983 4 0.0000 0.924 0.000 0.000 0.000 1.000 0.000
#> GSM152984 4 0.6243 0.202 0.000 0.388 0.088 0.504 0.020
#> GSM152985 4 0.3888 0.783 0.120 0.000 0.000 0.804 0.076
#> GSM152986 4 0.0000 0.924 0.000 0.000 0.000 1.000 0.000
#> GSM152987 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152988 4 0.1571 0.898 0.000 0.060 0.000 0.936 0.004
#> GSM152989 1 0.0794 0.956 0.972 0.000 0.000 0.000 0.028
#> GSM152990 3 0.0000 0.912 0.000 0.000 1.000 0.000 0.000
#> GSM152991 3 0.1965 0.894 0.000 0.000 0.904 0.000 0.096
#> GSM187524 1 0.0162 0.976 0.996 0.000 0.000 0.000 0.004
#> GSM187525 1 0.0162 0.976 0.996 0.000 0.000 0.000 0.004
#> GSM187526 1 0.0162 0.976 0.996 0.000 0.000 0.000 0.004
#> GSM187527 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152856 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152857 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152858 1 0.0162 0.976 0.996 0.000 0.000 0.000 0.004
#> GSM152859 1 0.0162 0.976 0.996 0.000 0.000 0.000 0.004
#> GSM152860 1 0.0162 0.976 0.996 0.000 0.000 0.000 0.004
#> GSM152861 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152862 1 0.0162 0.976 0.996 0.000 0.000 0.000 0.004
#> GSM152863 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152864 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152865 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152866 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152867 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152868 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152870 1 0.0162 0.976 0.996 0.000 0.000 0.000 0.004
#> GSM152871 1 0.0162 0.976 0.996 0.000 0.000 0.000 0.004
#> GSM152872 1 0.0162 0.976 0.996 0.000 0.000 0.000 0.004
#> GSM152873 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152875 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152876 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152877 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152878 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152879 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.977 1.000 0.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.1387 0.81498 0.000 0.932 0.068 0.000 0.000 0.000
#> GSM152805 5 0.2019 0.67291 0.000 0.000 0.088 0.000 0.900 0.012
#> GSM152806 5 0.0405 0.67775 0.000 0.000 0.008 0.000 0.988 0.004
#> GSM152807 2 0.0865 0.82220 0.000 0.964 0.036 0.000 0.000 0.000
#> GSM152808 5 0.0146 0.67600 0.000 0.000 0.000 0.000 0.996 0.004
#> GSM152809 2 0.0291 0.82396 0.000 0.992 0.004 0.000 0.000 0.004
#> GSM152810 6 0.4939 0.46231 0.000 0.000 0.064 0.000 0.440 0.496
#> GSM152811 5 0.0909 0.65978 0.000 0.000 0.012 0.000 0.968 0.020
#> GSM152812 2 0.0725 0.82183 0.000 0.976 0.012 0.000 0.000 0.012
#> GSM152813 2 0.1387 0.81479 0.000 0.932 0.068 0.000 0.000 0.000
#> GSM152814 2 0.1556 0.81035 0.000 0.920 0.080 0.000 0.000 0.000
#> GSM152815 2 0.0790 0.82276 0.000 0.968 0.032 0.000 0.000 0.000
#> GSM152816 5 0.4015 0.56202 0.000 0.000 0.372 0.000 0.616 0.012
#> GSM152817 5 0.0146 0.67600 0.000 0.000 0.000 0.000 0.996 0.004
#> GSM152818 5 0.0405 0.67775 0.000 0.000 0.008 0.000 0.988 0.004
#> GSM152819 5 0.3819 0.46254 0.000 0.000 0.372 0.000 0.624 0.004
#> GSM152820 5 0.4354 0.30454 0.000 0.000 0.144 0.000 0.724 0.132
#> GSM152821 6 0.6193 0.24967 0.000 0.088 0.420 0.000 0.060 0.432
#> GSM153115 4 0.3603 0.77178 0.000 0.124 0.056 0.808 0.000 0.012
#> GSM153116 5 0.3950 0.31761 0.000 0.000 0.432 0.000 0.564 0.004
#> GSM153117 3 0.4629 0.43116 0.000 0.052 0.680 0.000 0.252 0.016
#> GSM153118 3 0.4467 0.03594 0.000 0.480 0.496 0.000 0.020 0.004
#> GSM153119 5 0.0725 0.66482 0.000 0.000 0.012 0.000 0.976 0.012
#> GSM153120 4 0.2595 0.80256 0.000 0.000 0.004 0.836 0.000 0.160
#> GSM153121 5 0.4084 0.53797 0.000 0.000 0.400 0.000 0.588 0.012
#> GSM153122 5 0.0291 0.67408 0.000 0.000 0.004 0.000 0.992 0.004
#> GSM153123 2 0.2941 0.70415 0.000 0.780 0.220 0.000 0.000 0.000
#> GSM153124 4 0.5431 0.36647 0.000 0.356 0.084 0.544 0.000 0.016
#> GSM153125 4 0.3139 0.80428 0.000 0.084 0.056 0.848 0.000 0.012
#> GSM153126 5 0.3141 0.64589 0.000 0.000 0.200 0.000 0.788 0.012
#> GSM153127 2 0.1549 0.81594 0.000 0.936 0.044 0.000 0.000 0.020
#> GSM153128 6 0.4695 0.45359 0.000 0.000 0.044 0.000 0.448 0.508
#> GSM153129 3 0.4536 0.43379 0.000 0.076 0.712 0.000 0.200 0.012
#> GSM153130 5 0.3784 0.60027 0.000 0.000 0.308 0.000 0.680 0.012
#> GSM153131 5 0.4136 0.50568 0.000 0.000 0.428 0.000 0.560 0.012
#> GSM153132 3 0.4224 0.00591 0.000 0.000 0.552 0.000 0.432 0.016
#> GSM153133 3 0.6137 -0.29207 0.000 0.092 0.436 0.000 0.052 0.420
#> GSM153134 3 0.4343 0.36701 0.000 0.380 0.592 0.000 0.028 0.000
#> GSM153135 2 0.1245 0.82074 0.000 0.952 0.032 0.000 0.000 0.016
#> GSM153136 4 0.0260 0.85688 0.000 0.000 0.008 0.992 0.000 0.000
#> GSM153137 2 0.5106 0.44665 0.000 0.636 0.020 0.076 0.000 0.268
#> GSM153138 6 0.2653 0.60036 0.000 0.100 0.028 0.004 0.000 0.868
#> GSM153139 5 0.4109 0.52557 0.000 0.000 0.412 0.000 0.576 0.012
#> GSM153140 2 0.2113 0.80450 0.000 0.896 0.092 0.008 0.000 0.004
#> GSM153141 2 0.0291 0.82357 0.000 0.992 0.004 0.000 0.000 0.004
#> GSM153142 5 0.0291 0.67720 0.000 0.000 0.004 0.000 0.992 0.004
#> GSM153143 2 0.5011 0.44453 0.000 0.620 0.116 0.000 0.000 0.264
#> GSM153144 2 0.3636 0.55781 0.000 0.676 0.320 0.000 0.000 0.004
#> GSM153145 5 0.0291 0.67720 0.000 0.000 0.004 0.000 0.992 0.004
#> GSM153146 6 0.6193 0.24967 0.000 0.088 0.420 0.000 0.060 0.432
#> GSM153147 3 0.5812 -0.24299 0.000 0.024 0.464 0.000 0.100 0.412
#> GSM153148 2 0.2030 0.80447 0.000 0.908 0.064 0.000 0.000 0.028
#> GSM153149 6 0.6039 0.25999 0.000 0.044 0.428 0.000 0.092 0.436
#> GSM153150 4 0.2772 0.79219 0.000 0.000 0.004 0.816 0.000 0.180
#> GSM153151 6 0.5285 0.52594 0.000 0.012 0.260 0.000 0.112 0.616
#> GSM153152 3 0.4471 0.40376 0.000 0.028 0.684 0.000 0.264 0.024
#> GSM153153 3 0.4833 0.37807 0.000 0.360 0.588 0.000 0.036 0.016
#> GSM153154 3 0.4242 -0.02571 0.000 0.000 0.536 0.000 0.448 0.016
#> GSM153155 6 0.5522 0.40925 0.000 0.256 0.188 0.000 0.000 0.556
#> GSM153156 5 0.2190 0.65991 0.000 0.000 0.060 0.000 0.900 0.040
#> GSM153157 5 0.0909 0.65978 0.000 0.000 0.012 0.000 0.968 0.020
#> GSM153158 5 0.3955 0.32526 0.000 0.000 0.436 0.000 0.560 0.004
#> GSM153159 5 0.0291 0.67720 0.000 0.000 0.004 0.000 0.992 0.004
#> GSM153160 5 0.4129 0.51256 0.000 0.000 0.424 0.000 0.564 0.012
#> GSM153161 2 0.0909 0.82077 0.000 0.968 0.012 0.000 0.000 0.020
#> GSM153162 3 0.4268 0.57009 0.000 0.200 0.732 0.000 0.056 0.012
#> GSM153163 5 0.4129 0.51256 0.000 0.000 0.424 0.000 0.564 0.012
#> GSM153164 3 0.4828 0.50154 0.000 0.292 0.640 0.000 0.052 0.016
#> GSM153165 5 0.4141 0.49751 0.000 0.000 0.432 0.000 0.556 0.012
#> GSM153166 3 0.4330 0.44934 0.000 0.332 0.632 0.000 0.036 0.000
#> GSM153167 3 0.3789 0.56505 0.000 0.196 0.760 0.000 0.040 0.004
#> GSM153168 5 0.0146 0.67600 0.000 0.000 0.000 0.000 0.996 0.004
#> GSM153169 5 0.2489 0.66618 0.000 0.000 0.128 0.000 0.860 0.012
#> GSM153170 3 0.4066 -0.04625 0.000 0.000 0.596 0.000 0.392 0.012
#> GSM153171 4 0.3240 0.79898 0.000 0.092 0.056 0.840 0.000 0.012
#> GSM153172 2 0.2300 0.78321 0.000 0.856 0.144 0.000 0.000 0.000
#> GSM153173 5 0.4129 0.51079 0.000 0.000 0.424 0.000 0.564 0.012
#> GSM153174 2 0.4258 0.15812 0.000 0.516 0.468 0.000 0.000 0.016
#> GSM153175 4 0.1625 0.84320 0.000 0.000 0.060 0.928 0.000 0.012
#> GSM153176 5 0.4272 0.57579 0.000 0.000 0.240 0.004 0.704 0.052
#> GSM153177 3 0.4371 0.43416 0.000 0.344 0.620 0.000 0.036 0.000
#> GSM152931 4 0.1296 0.84931 0.000 0.004 0.032 0.952 0.000 0.012
#> GSM152932 2 0.3950 0.24685 0.000 0.564 0.432 0.000 0.004 0.000
#> GSM152933 3 0.5226 0.39836 0.000 0.336 0.584 0.000 0.048 0.032
#> GSM152934 6 0.2213 0.60558 0.000 0.000 0.032 0.048 0.012 0.908
#> GSM152935 3 0.4829 0.51109 0.000 0.280 0.648 0.000 0.056 0.016
#> GSM152936 4 0.2805 0.79008 0.000 0.000 0.004 0.812 0.000 0.184
#> GSM152937 6 0.4587 0.55076 0.000 0.000 0.048 0.000 0.356 0.596
#> GSM152938 5 0.4101 0.53169 0.000 0.000 0.408 0.000 0.580 0.012
#> GSM152939 4 0.3500 0.77825 0.000 0.120 0.052 0.816 0.000 0.012
#> GSM152940 4 0.1327 0.84698 0.000 0.000 0.000 0.936 0.000 0.064
#> GSM152941 1 0.2066 0.92039 0.908 0.000 0.052 0.000 0.000 0.040
#> GSM152942 5 0.4123 0.51712 0.000 0.000 0.420 0.000 0.568 0.012
#> GSM152943 6 0.1364 0.59856 0.000 0.004 0.004 0.048 0.000 0.944
#> GSM152944 5 0.4047 0.52694 0.000 0.000 0.384 0.000 0.604 0.012
#> GSM152945 2 0.4652 0.44224 0.000 0.640 0.072 0.000 0.000 0.288
#> GSM152946 2 0.2213 0.80034 0.000 0.888 0.100 0.008 0.000 0.004
#> GSM152947 4 0.0713 0.85611 0.000 0.000 0.000 0.972 0.000 0.028
#> GSM152948 2 0.0713 0.82303 0.000 0.972 0.028 0.000 0.000 0.000
#> GSM152949 3 0.4212 0.02041 0.000 0.000 0.560 0.000 0.424 0.016
#> GSM152950 3 0.4529 -0.08970 0.000 0.000 0.508 0.000 0.460 0.032
#> GSM152951 2 0.1010 0.82176 0.000 0.960 0.036 0.004 0.000 0.000
#> GSM152952 2 0.0909 0.82077 0.000 0.968 0.012 0.000 0.000 0.020
#> GSM152953 2 0.1257 0.82014 0.000 0.952 0.028 0.000 0.000 0.020
#> GSM152954 4 0.2838 0.78741 0.000 0.000 0.004 0.808 0.000 0.188
#> GSM152955 6 0.4203 0.57998 0.000 0.000 0.032 0.000 0.316 0.652
#> GSM152956 2 0.1003 0.82056 0.000 0.964 0.016 0.000 0.000 0.020
#> GSM152957 1 0.4803 0.77001 0.736 0.000 0.064 0.088 0.000 0.112
#> GSM152958 4 0.0713 0.85580 0.000 0.000 0.000 0.972 0.000 0.028
#> GSM152959 1 0.6260 0.48840 0.552 0.000 0.056 0.160 0.000 0.232
#> GSM152960 6 0.1946 0.57038 0.004 0.000 0.012 0.072 0.000 0.912
#> GSM152961 4 0.0547 0.85651 0.000 0.000 0.000 0.980 0.000 0.020
#> GSM152962 6 0.5507 0.50732 0.000 0.000 0.156 0.000 0.308 0.536
#> GSM152963 2 0.2058 0.80365 0.000 0.908 0.056 0.000 0.000 0.036
#> GSM152964 6 0.4921 0.48221 0.000 0.000 0.064 0.000 0.420 0.516
#> GSM152965 6 0.5931 0.37862 0.000 0.056 0.364 0.000 0.072 0.508
#> GSM152966 4 0.0363 0.85628 0.000 0.000 0.012 0.988 0.000 0.000
#> GSM152967 2 0.4403 0.54898 0.000 0.648 0.304 0.000 0.000 0.048
#> GSM152968 3 0.4224 0.00836 0.000 0.000 0.552 0.000 0.432 0.016
#> GSM152969 4 0.0520 0.85765 0.000 0.000 0.008 0.984 0.000 0.008
#> GSM152970 1 0.5097 0.71950 0.704 0.000 0.052 0.132 0.000 0.112
#> GSM152971 4 0.0260 0.85688 0.000 0.000 0.008 0.992 0.000 0.000
#> GSM152972 4 0.0937 0.85356 0.000 0.000 0.000 0.960 0.000 0.040
#> GSM152973 3 0.7071 0.26385 0.000 0.160 0.536 0.148 0.132 0.024
#> GSM152974 2 0.3330 0.60955 0.000 0.716 0.284 0.000 0.000 0.000
#> GSM152975 2 0.4787 0.58571 0.000 0.672 0.104 0.220 0.000 0.004
#> GSM152976 4 0.1913 0.83968 0.000 0.000 0.080 0.908 0.000 0.012
#> GSM152977 4 0.4335 0.74722 0.024 0.000 0.056 0.744 0.000 0.176
#> GSM152978 4 0.2595 0.80256 0.000 0.000 0.004 0.836 0.000 0.160
#> GSM152979 5 0.4129 0.51256 0.000 0.000 0.424 0.000 0.564 0.012
#> GSM152980 6 0.2838 0.60374 0.000 0.072 0.024 0.032 0.000 0.872
#> GSM152981 5 0.1257 0.64413 0.000 0.000 0.020 0.000 0.952 0.028
#> GSM152982 4 0.4280 0.70760 0.000 0.000 0.056 0.708 0.004 0.232
#> GSM152983 4 0.0777 0.85576 0.000 0.000 0.024 0.972 0.000 0.004
#> GSM152984 4 0.6278 0.21377 0.000 0.160 0.400 0.416 0.004 0.020
#> GSM152985 4 0.4894 0.68066 0.088 0.000 0.032 0.704 0.000 0.176
#> GSM152986 4 0.0260 0.85688 0.000 0.000 0.008 0.992 0.000 0.000
#> GSM152987 1 0.2001 0.92118 0.912 0.000 0.048 0.000 0.000 0.040
#> GSM152988 4 0.3154 0.81142 0.000 0.068 0.072 0.848 0.000 0.012
#> GSM152989 1 0.3279 0.86340 0.828 0.000 0.060 0.004 0.000 0.108
#> GSM152990 5 0.4136 0.50568 0.000 0.000 0.428 0.000 0.560 0.012
#> GSM152991 5 0.1480 0.64337 0.000 0.000 0.040 0.000 0.940 0.020
#> GSM187524 1 0.2066 0.92025 0.908 0.000 0.052 0.000 0.000 0.040
#> GSM187525 1 0.2066 0.92025 0.908 0.000 0.052 0.000 0.000 0.040
#> GSM187526 1 0.2066 0.92025 0.908 0.000 0.052 0.000 0.000 0.040
#> GSM187527 1 0.0547 0.93058 0.980 0.000 0.020 0.000 0.000 0.000
#> GSM152856 1 0.0547 0.93058 0.980 0.000 0.020 0.000 0.000 0.000
#> GSM152857 1 0.0547 0.93058 0.980 0.000 0.020 0.000 0.000 0.000
#> GSM152858 1 0.2066 0.92025 0.908 0.000 0.052 0.000 0.000 0.040
#> GSM152859 1 0.2134 0.91863 0.904 0.000 0.052 0.000 0.000 0.044
#> GSM152860 1 0.2066 0.92025 0.908 0.000 0.052 0.000 0.000 0.040
#> GSM152861 1 0.0146 0.93264 0.996 0.000 0.004 0.000 0.000 0.000
#> GSM152862 1 0.2066 0.92025 0.908 0.000 0.052 0.000 0.000 0.040
#> GSM152863 1 0.0000 0.93265 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152864 1 0.0000 0.93265 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152865 1 0.0146 0.93264 0.996 0.000 0.004 0.000 0.000 0.000
#> GSM152866 1 0.0547 0.93058 0.980 0.000 0.020 0.000 0.000 0.000
#> GSM152867 1 0.0000 0.93265 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152868 1 0.0000 0.93265 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152869 1 0.0000 0.93265 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152870 1 0.2066 0.92025 0.908 0.000 0.052 0.000 0.000 0.040
#> GSM152871 1 0.1995 0.92131 0.912 0.000 0.052 0.000 0.000 0.036
#> GSM152872 1 0.2066 0.92025 0.908 0.000 0.052 0.000 0.000 0.040
#> GSM152873 1 0.0547 0.93058 0.980 0.000 0.020 0.000 0.000 0.000
#> GSM152874 1 0.0547 0.93058 0.980 0.000 0.020 0.000 0.000 0.000
#> GSM152875 1 0.0547 0.93058 0.980 0.000 0.020 0.000 0.000 0.000
#> GSM152876 1 0.0547 0.93058 0.980 0.000 0.020 0.000 0.000 0.000
#> GSM152877 1 0.0547 0.93058 0.980 0.000 0.020 0.000 0.000 0.000
#> GSM152878 1 0.0547 0.93058 0.980 0.000 0.020 0.000 0.000 0.000
#> GSM152879 1 0.0547 0.93058 0.980 0.000 0.020 0.000 0.000 0.000
#> GSM152880 1 0.0547 0.93058 0.980 0.000 0.020 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> ATC:skmeans 170 7.60e-15 2
#> ATC:skmeans 158 5.64e-20 3
#> ATC:skmeans 169 6.79e-27 4
#> ATC:skmeans 165 1.22e-23 5
#> ATC:skmeans 132 1.05e-19 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "pam"]
# you can also extract it by
# res = res_list["ATC:pam"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'pam' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.980 0.992 0.2921 0.709 0.709
#> 3 3 0.634 0.839 0.916 0.9897 0.705 0.588
#> 4 4 0.632 0.776 0.834 0.0442 0.991 0.980
#> 5 5 0.755 0.819 0.906 0.2151 0.766 0.487
#> 6 6 0.784 0.820 0.892 0.0268 0.988 0.952
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.000 0.9949 0.000 1.000
#> GSM152805 2 0.000 0.9949 0.000 1.000
#> GSM152806 2 0.000 0.9949 0.000 1.000
#> GSM152807 2 0.000 0.9949 0.000 1.000
#> GSM152808 2 0.000 0.9949 0.000 1.000
#> GSM152809 2 0.000 0.9949 0.000 1.000
#> GSM152810 2 0.000 0.9949 0.000 1.000
#> GSM152811 2 0.000 0.9949 0.000 1.000
#> GSM152812 2 0.000 0.9949 0.000 1.000
#> GSM152813 2 0.000 0.9949 0.000 1.000
#> GSM152814 2 0.000 0.9949 0.000 1.000
#> GSM152815 2 0.000 0.9949 0.000 1.000
#> GSM152816 2 0.000 0.9949 0.000 1.000
#> GSM152817 2 0.000 0.9949 0.000 1.000
#> GSM152818 2 0.000 0.9949 0.000 1.000
#> GSM152819 2 0.000 0.9949 0.000 1.000
#> GSM152820 2 0.000 0.9949 0.000 1.000
#> GSM152821 2 0.000 0.9949 0.000 1.000
#> GSM153115 2 0.000 0.9949 0.000 1.000
#> GSM153116 2 0.000 0.9949 0.000 1.000
#> GSM153117 2 0.000 0.9949 0.000 1.000
#> GSM153118 2 0.000 0.9949 0.000 1.000
#> GSM153119 2 0.000 0.9949 0.000 1.000
#> GSM153120 2 0.000 0.9949 0.000 1.000
#> GSM153121 2 0.000 0.9949 0.000 1.000
#> GSM153122 2 0.000 0.9949 0.000 1.000
#> GSM153123 2 0.000 0.9949 0.000 1.000
#> GSM153124 2 0.000 0.9949 0.000 1.000
#> GSM153125 2 0.000 0.9949 0.000 1.000
#> GSM153126 2 0.000 0.9949 0.000 1.000
#> GSM153127 2 0.000 0.9949 0.000 1.000
#> GSM153128 2 0.000 0.9949 0.000 1.000
#> GSM153129 2 0.000 0.9949 0.000 1.000
#> GSM153130 2 0.000 0.9949 0.000 1.000
#> GSM153131 2 0.000 0.9949 0.000 1.000
#> GSM153132 2 0.000 0.9949 0.000 1.000
#> GSM153133 2 0.000 0.9949 0.000 1.000
#> GSM153134 2 0.000 0.9949 0.000 1.000
#> GSM153135 2 0.000 0.9949 0.000 1.000
#> GSM153136 2 0.000 0.9949 0.000 1.000
#> GSM153137 2 0.000 0.9949 0.000 1.000
#> GSM153138 2 0.000 0.9949 0.000 1.000
#> GSM153139 2 0.000 0.9949 0.000 1.000
#> GSM153140 2 0.000 0.9949 0.000 1.000
#> GSM153141 2 0.000 0.9949 0.000 1.000
#> GSM153142 2 0.000 0.9949 0.000 1.000
#> GSM153143 2 0.000 0.9949 0.000 1.000
#> GSM153144 2 0.000 0.9949 0.000 1.000
#> GSM153145 2 0.000 0.9949 0.000 1.000
#> GSM153146 2 0.000 0.9949 0.000 1.000
#> GSM153147 2 0.000 0.9949 0.000 1.000
#> GSM153148 2 0.000 0.9949 0.000 1.000
#> GSM153149 2 0.000 0.9949 0.000 1.000
#> GSM153150 2 0.000 0.9949 0.000 1.000
#> GSM153151 2 0.000 0.9949 0.000 1.000
#> GSM153152 2 0.000 0.9949 0.000 1.000
#> GSM153153 2 0.000 0.9949 0.000 1.000
#> GSM153154 2 0.000 0.9949 0.000 1.000
#> GSM153155 2 0.000 0.9949 0.000 1.000
#> GSM153156 2 0.000 0.9949 0.000 1.000
#> GSM153157 2 0.000 0.9949 0.000 1.000
#> GSM153158 2 0.000 0.9949 0.000 1.000
#> GSM153159 2 0.000 0.9949 0.000 1.000
#> GSM153160 2 0.000 0.9949 0.000 1.000
#> GSM153161 2 0.000 0.9949 0.000 1.000
#> GSM153162 2 0.000 0.9949 0.000 1.000
#> GSM153163 2 0.000 0.9949 0.000 1.000
#> GSM153164 2 0.000 0.9949 0.000 1.000
#> GSM153165 2 0.000 0.9949 0.000 1.000
#> GSM153166 2 0.000 0.9949 0.000 1.000
#> GSM153167 2 0.000 0.9949 0.000 1.000
#> GSM153168 2 0.000 0.9949 0.000 1.000
#> GSM153169 2 0.000 0.9949 0.000 1.000
#> GSM153170 2 0.000 0.9949 0.000 1.000
#> GSM153171 2 0.000 0.9949 0.000 1.000
#> GSM153172 2 0.000 0.9949 0.000 1.000
#> GSM153173 2 0.000 0.9949 0.000 1.000
#> GSM153174 2 0.000 0.9949 0.000 1.000
#> GSM153175 2 0.000 0.9949 0.000 1.000
#> GSM153176 2 0.000 0.9949 0.000 1.000
#> GSM153177 2 0.000 0.9949 0.000 1.000
#> GSM152931 2 0.000 0.9949 0.000 1.000
#> GSM152932 2 0.000 0.9949 0.000 1.000
#> GSM152933 2 0.000 0.9949 0.000 1.000
#> GSM152934 2 0.000 0.9949 0.000 1.000
#> GSM152935 2 0.000 0.9949 0.000 1.000
#> GSM152936 2 0.000 0.9949 0.000 1.000
#> GSM152937 2 0.000 0.9949 0.000 1.000
#> GSM152938 2 0.000 0.9949 0.000 1.000
#> GSM152939 2 0.000 0.9949 0.000 1.000
#> GSM152940 2 0.000 0.9949 0.000 1.000
#> GSM152941 1 0.000 0.9777 1.000 0.000
#> GSM152942 2 0.000 0.9949 0.000 1.000
#> GSM152943 2 0.000 0.9949 0.000 1.000
#> GSM152944 2 0.000 0.9949 0.000 1.000
#> GSM152945 2 0.000 0.9949 0.000 1.000
#> GSM152946 2 0.000 0.9949 0.000 1.000
#> GSM152947 2 0.000 0.9949 0.000 1.000
#> GSM152948 2 0.000 0.9949 0.000 1.000
#> GSM152949 2 0.000 0.9949 0.000 1.000
#> GSM152950 2 0.000 0.9949 0.000 1.000
#> GSM152951 2 0.000 0.9949 0.000 1.000
#> GSM152952 2 0.000 0.9949 0.000 1.000
#> GSM152953 2 0.000 0.9949 0.000 1.000
#> GSM152954 2 0.000 0.9949 0.000 1.000
#> GSM152955 2 0.000 0.9949 0.000 1.000
#> GSM152956 2 0.000 0.9949 0.000 1.000
#> GSM152957 2 0.000 0.9949 0.000 1.000
#> GSM152958 2 0.000 0.9949 0.000 1.000
#> GSM152959 2 0.000 0.9949 0.000 1.000
#> GSM152960 2 0.000 0.9949 0.000 1.000
#> GSM152961 2 0.000 0.9949 0.000 1.000
#> GSM152962 2 0.000 0.9949 0.000 1.000
#> GSM152963 2 0.000 0.9949 0.000 1.000
#> GSM152964 2 0.000 0.9949 0.000 1.000
#> GSM152965 2 0.000 0.9949 0.000 1.000
#> GSM152966 2 0.000 0.9949 0.000 1.000
#> GSM152967 2 0.000 0.9949 0.000 1.000
#> GSM152968 2 0.000 0.9949 0.000 1.000
#> GSM152969 2 0.000 0.9949 0.000 1.000
#> GSM152970 2 0.000 0.9949 0.000 1.000
#> GSM152971 2 0.000 0.9949 0.000 1.000
#> GSM152972 2 0.000 0.9949 0.000 1.000
#> GSM152973 2 0.000 0.9949 0.000 1.000
#> GSM152974 2 0.000 0.9949 0.000 1.000
#> GSM152975 2 0.000 0.9949 0.000 1.000
#> GSM152976 2 0.000 0.9949 0.000 1.000
#> GSM152977 2 0.000 0.9949 0.000 1.000
#> GSM152978 2 0.000 0.9949 0.000 1.000
#> GSM152979 2 0.000 0.9949 0.000 1.000
#> GSM152980 2 0.000 0.9949 0.000 1.000
#> GSM152981 2 0.000 0.9949 0.000 1.000
#> GSM152982 2 0.000 0.9949 0.000 1.000
#> GSM152983 2 0.000 0.9949 0.000 1.000
#> GSM152984 2 0.000 0.9949 0.000 1.000
#> GSM152985 2 0.518 0.8633 0.116 0.884
#> GSM152986 2 0.000 0.9949 0.000 1.000
#> GSM152987 1 0.000 0.9777 1.000 0.000
#> GSM152988 2 0.000 0.9949 0.000 1.000
#> GSM152989 1 0.999 0.0798 0.520 0.480
#> GSM152990 2 0.000 0.9949 0.000 1.000
#> GSM152991 2 0.000 0.9949 0.000 1.000
#> GSM187524 1 0.000 0.9777 1.000 0.000
#> GSM187525 1 0.000 0.9777 1.000 0.000
#> GSM187526 1 0.000 0.9777 1.000 0.000
#> GSM187527 2 0.891 0.5437 0.308 0.692
#> GSM152856 1 0.000 0.9777 1.000 0.000
#> GSM152857 2 0.844 0.6168 0.272 0.728
#> GSM152858 1 0.000 0.9777 1.000 0.000
#> GSM152859 1 0.000 0.9777 1.000 0.000
#> GSM152860 1 0.000 0.9777 1.000 0.000
#> GSM152861 1 0.000 0.9777 1.000 0.000
#> GSM152862 1 0.000 0.9777 1.000 0.000
#> GSM152863 1 0.000 0.9777 1.000 0.000
#> GSM152864 1 0.000 0.9777 1.000 0.000
#> GSM152865 1 0.000 0.9777 1.000 0.000
#> GSM152866 1 0.000 0.9777 1.000 0.000
#> GSM152867 1 0.000 0.9777 1.000 0.000
#> GSM152868 1 0.000 0.9777 1.000 0.000
#> GSM152869 1 0.000 0.9777 1.000 0.000
#> GSM152870 1 0.000 0.9777 1.000 0.000
#> GSM152871 1 0.000 0.9777 1.000 0.000
#> GSM152872 1 0.000 0.9777 1.000 0.000
#> GSM152873 1 0.000 0.9777 1.000 0.000
#> GSM152874 1 0.000 0.9777 1.000 0.000
#> GSM152875 1 0.000 0.9777 1.000 0.000
#> GSM152876 1 0.634 0.7997 0.840 0.160
#> GSM152877 1 0.000 0.9777 1.000 0.000
#> GSM152878 1 0.000 0.9777 1.000 0.000
#> GSM152879 1 0.000 0.9777 1.000 0.000
#> GSM152880 1 0.000 0.9777 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.3879 0.869 0.000 0.848 0.152
#> GSM152805 3 0.0000 0.914 0.000 0.000 1.000
#> GSM152806 3 0.0000 0.914 0.000 0.000 1.000
#> GSM152807 2 0.3879 0.869 0.000 0.848 0.152
#> GSM152808 3 0.0000 0.914 0.000 0.000 1.000
#> GSM152809 2 0.3340 0.875 0.000 0.880 0.120
#> GSM152810 2 0.6180 0.163 0.000 0.584 0.416
#> GSM152811 3 0.1289 0.889 0.000 0.032 0.968
#> GSM152812 2 0.3879 0.869 0.000 0.848 0.152
#> GSM152813 2 0.3879 0.869 0.000 0.848 0.152
#> GSM152814 2 0.3879 0.869 0.000 0.848 0.152
#> GSM152815 2 0.3879 0.869 0.000 0.848 0.152
#> GSM152816 3 0.0000 0.914 0.000 0.000 1.000
#> GSM152817 3 0.1289 0.889 0.000 0.032 0.968
#> GSM152818 3 0.0000 0.914 0.000 0.000 1.000
#> GSM152819 3 0.0000 0.914 0.000 0.000 1.000
#> GSM152820 2 0.4178 0.856 0.000 0.828 0.172
#> GSM152821 2 0.4062 0.862 0.000 0.836 0.164
#> GSM153115 2 0.1289 0.868 0.000 0.968 0.032
#> GSM153116 3 0.0237 0.911 0.000 0.004 0.996
#> GSM153117 3 0.0237 0.911 0.000 0.004 0.996
#> GSM153118 2 0.4062 0.862 0.000 0.836 0.164
#> GSM153119 3 0.0237 0.911 0.000 0.004 0.996
#> GSM153120 2 0.0000 0.870 0.000 1.000 0.000
#> GSM153121 3 0.6204 0.146 0.000 0.424 0.576
#> GSM153122 3 0.1289 0.889 0.000 0.032 0.968
#> GSM153123 2 0.4121 0.859 0.000 0.832 0.168
#> GSM153124 2 0.1289 0.868 0.000 0.968 0.032
#> GSM153125 2 0.1289 0.868 0.000 0.968 0.032
#> GSM153126 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153127 2 0.3340 0.875 0.000 0.880 0.120
#> GSM153128 3 0.4346 0.722 0.000 0.184 0.816
#> GSM153129 3 0.6180 0.140 0.000 0.416 0.584
#> GSM153130 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153131 2 0.4178 0.856 0.000 0.828 0.172
#> GSM153132 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153133 2 0.3482 0.873 0.000 0.872 0.128
#> GSM153134 3 0.6154 0.168 0.000 0.408 0.592
#> GSM153135 2 0.3340 0.875 0.000 0.880 0.120
#> GSM153136 2 0.0000 0.870 0.000 1.000 0.000
#> GSM153137 2 0.0000 0.870 0.000 1.000 0.000
#> GSM153138 2 0.2066 0.874 0.000 0.940 0.060
#> GSM153139 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153140 2 0.3879 0.869 0.000 0.848 0.152
#> GSM153141 2 0.3816 0.870 0.000 0.852 0.148
#> GSM153142 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153143 2 0.3340 0.875 0.000 0.880 0.120
#> GSM153144 2 0.4002 0.865 0.000 0.840 0.160
#> GSM153145 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153146 2 0.4002 0.865 0.000 0.840 0.160
#> GSM153147 2 0.3482 0.873 0.000 0.872 0.128
#> GSM153148 2 0.3340 0.875 0.000 0.880 0.120
#> GSM153149 2 0.4291 0.850 0.000 0.820 0.180
#> GSM153150 2 0.0000 0.870 0.000 1.000 0.000
#> GSM153151 2 0.3482 0.873 0.000 0.872 0.128
#> GSM153152 2 0.3752 0.866 0.000 0.856 0.144
#> GSM153153 2 0.4235 0.853 0.000 0.824 0.176
#> GSM153154 3 0.1289 0.889 0.000 0.032 0.968
#> GSM153155 2 0.3267 0.876 0.000 0.884 0.116
#> GSM153156 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153157 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153158 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153159 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153160 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153161 2 0.3412 0.875 0.000 0.876 0.124
#> GSM153162 2 0.4555 0.822 0.000 0.800 0.200
#> GSM153163 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153164 2 0.6299 0.266 0.000 0.524 0.476
#> GSM153165 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153166 3 0.6154 0.168 0.000 0.408 0.592
#> GSM153167 2 0.4002 0.865 0.000 0.840 0.160
#> GSM153168 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153169 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153170 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153171 2 0.0424 0.870 0.000 0.992 0.008
#> GSM153172 2 0.3879 0.869 0.000 0.848 0.152
#> GSM153173 3 0.0000 0.914 0.000 0.000 1.000
#> GSM153174 2 0.3340 0.875 0.000 0.880 0.120
#> GSM153175 2 0.0000 0.870 0.000 1.000 0.000
#> GSM153176 2 0.5988 0.300 0.000 0.632 0.368
#> GSM153177 2 0.6280 0.320 0.000 0.540 0.460
#> GSM152931 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152932 2 0.3941 0.867 0.000 0.844 0.156
#> GSM152933 2 0.4235 0.853 0.000 0.824 0.176
#> GSM152934 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152935 2 0.5926 0.587 0.000 0.644 0.356
#> GSM152936 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152937 2 0.5560 0.536 0.000 0.700 0.300
#> GSM152938 3 0.6305 -0.137 0.000 0.484 0.516
#> GSM152939 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152940 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152941 1 0.1529 0.949 0.960 0.040 0.000
#> GSM152942 2 0.4452 0.830 0.000 0.808 0.192
#> GSM152943 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152944 3 0.0000 0.914 0.000 0.000 1.000
#> GSM152945 2 0.3340 0.875 0.000 0.880 0.120
#> GSM152946 2 0.3879 0.869 0.000 0.848 0.152
#> GSM152947 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152948 2 0.3879 0.869 0.000 0.848 0.152
#> GSM152949 2 0.6280 0.258 0.000 0.540 0.460
#> GSM152950 2 0.3619 0.870 0.000 0.864 0.136
#> GSM152951 2 0.1964 0.877 0.000 0.944 0.056
#> GSM152952 2 0.3752 0.872 0.000 0.856 0.144
#> GSM152953 2 0.3879 0.869 0.000 0.848 0.152
#> GSM152954 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152955 2 0.0592 0.866 0.000 0.988 0.012
#> GSM152956 2 0.3879 0.869 0.000 0.848 0.152
#> GSM152957 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152958 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152959 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152960 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152961 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152962 2 0.4452 0.831 0.000 0.808 0.192
#> GSM152963 2 0.3879 0.869 0.000 0.848 0.152
#> GSM152964 2 0.6180 0.163 0.000 0.584 0.416
#> GSM152965 2 0.3482 0.873 0.000 0.872 0.128
#> GSM152966 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152967 2 0.3340 0.875 0.000 0.880 0.120
#> GSM152968 3 0.0000 0.914 0.000 0.000 1.000
#> GSM152969 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152970 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152971 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152972 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152973 2 0.1289 0.868 0.000 0.968 0.032
#> GSM152974 2 0.4062 0.862 0.000 0.836 0.164
#> GSM152975 2 0.1964 0.877 0.000 0.944 0.056
#> GSM152976 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152977 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152978 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152979 3 0.0000 0.914 0.000 0.000 1.000
#> GSM152980 2 0.2537 0.876 0.000 0.920 0.080
#> GSM152981 3 0.1289 0.889 0.000 0.032 0.968
#> GSM152982 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152983 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152984 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152985 2 0.0237 0.868 0.004 0.996 0.000
#> GSM152986 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152987 1 0.1163 0.960 0.972 0.028 0.000
#> GSM152988 2 0.0000 0.870 0.000 1.000 0.000
#> GSM152989 2 0.4291 0.711 0.180 0.820 0.000
#> GSM152990 3 0.0000 0.914 0.000 0.000 1.000
#> GSM152991 3 0.1289 0.889 0.000 0.032 0.968
#> GSM187524 1 0.0000 0.982 1.000 0.000 0.000
#> GSM187525 1 0.0000 0.982 1.000 0.000 0.000
#> GSM187526 1 0.0000 0.982 1.000 0.000 0.000
#> GSM187527 2 0.6027 0.555 0.272 0.712 0.016
#> GSM152856 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152857 2 0.7634 0.564 0.232 0.668 0.100
#> GSM152858 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152859 1 0.0237 0.978 0.996 0.004 0.000
#> GSM152860 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152861 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152862 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152863 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152864 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152866 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152867 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152870 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152871 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152873 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152874 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152875 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152876 1 0.5810 0.510 0.664 0.336 0.000
#> GSM152877 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152878 1 0.1163 0.960 0.972 0.028 0.000
#> GSM152879 1 0.0000 0.982 1.000 0.000 0.000
#> GSM152880 1 0.0000 0.982 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.3257 0.8553 0.000 0.844 0.152 NA
#> GSM152805 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM152806 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM152807 2 0.3257 0.8553 0.000 0.844 0.152 NA
#> GSM152808 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM152809 2 0.2593 0.8653 0.000 0.892 0.104 NA
#> GSM152810 2 0.5543 0.1183 0.000 0.556 0.424 NA
#> GSM152811 3 0.1389 0.8508 0.000 0.048 0.952 NA
#> GSM152812 2 0.3257 0.8553 0.000 0.844 0.152 NA
#> GSM152813 2 0.3257 0.8553 0.000 0.844 0.152 NA
#> GSM152814 2 0.3257 0.8553 0.000 0.844 0.152 NA
#> GSM152815 2 0.3257 0.8553 0.000 0.844 0.152 NA
#> GSM152816 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM152817 3 0.1302 0.8549 0.000 0.044 0.956 NA
#> GSM152818 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM152819 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM152820 2 0.3266 0.8469 0.000 0.832 0.168 NA
#> GSM152821 2 0.3355 0.8511 0.000 0.836 0.160 NA
#> GSM153115 2 0.2313 0.8565 0.000 0.924 0.044 NA
#> GSM153116 3 0.0188 0.8926 0.000 0.004 0.996 NA
#> GSM153117 3 0.0188 0.8923 0.000 0.004 0.996 NA
#> GSM153118 2 0.3355 0.8511 0.000 0.836 0.160 NA
#> GSM153119 3 0.0188 0.8926 0.000 0.004 0.996 NA
#> GSM153120 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM153121 3 0.4977 0.0358 0.000 0.460 0.540 NA
#> GSM153122 3 0.1389 0.8508 0.000 0.048 0.952 NA
#> GSM153123 2 0.3448 0.8455 0.000 0.828 0.168 NA
#> GSM153124 2 0.2399 0.8559 0.000 0.920 0.048 NA
#> GSM153125 2 0.2399 0.8559 0.000 0.920 0.048 NA
#> GSM153126 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153127 2 0.2593 0.8653 0.000 0.892 0.104 NA
#> GSM153128 3 0.3400 0.6983 0.000 0.180 0.820 NA
#> GSM153129 3 0.4955 0.0532 0.000 0.444 0.556 NA
#> GSM153130 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153131 2 0.3311 0.8440 0.000 0.828 0.172 NA
#> GSM153132 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153133 2 0.2654 0.8646 0.000 0.888 0.108 NA
#> GSM153134 3 0.4948 0.0690 0.000 0.440 0.560 NA
#> GSM153135 2 0.2593 0.8653 0.000 0.892 0.104 NA
#> GSM153136 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM153137 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM153138 2 0.2644 0.8605 0.000 0.908 0.060 NA
#> GSM153139 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153140 2 0.3257 0.8553 0.000 0.844 0.152 NA
#> GSM153141 2 0.3208 0.8570 0.000 0.848 0.148 NA
#> GSM153142 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153143 2 0.2593 0.8653 0.000 0.892 0.104 NA
#> GSM153144 2 0.3306 0.8534 0.000 0.840 0.156 NA
#> GSM153145 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153146 2 0.3306 0.8534 0.000 0.840 0.156 NA
#> GSM153147 2 0.2654 0.8646 0.000 0.888 0.108 NA
#> GSM153148 2 0.2714 0.8650 0.000 0.884 0.112 NA
#> GSM153149 2 0.3494 0.8425 0.000 0.824 0.172 NA
#> GSM153150 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM153151 2 0.2654 0.8646 0.000 0.888 0.108 NA
#> GSM153152 2 0.2760 0.8583 0.000 0.872 0.128 NA
#> GSM153153 2 0.3356 0.8408 0.000 0.824 0.176 NA
#> GSM153154 3 0.1389 0.8508 0.000 0.048 0.952 NA
#> GSM153155 2 0.2530 0.8661 0.000 0.896 0.100 NA
#> GSM153156 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153157 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153158 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153159 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153160 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153161 2 0.2831 0.8640 0.000 0.876 0.120 NA
#> GSM153162 2 0.3356 0.8324 0.000 0.824 0.176 NA
#> GSM153163 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153164 2 0.4967 0.3209 0.000 0.548 0.452 NA
#> GSM153165 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153166 3 0.4948 0.0690 0.000 0.440 0.560 NA
#> GSM153167 2 0.3172 0.8526 0.000 0.840 0.160 NA
#> GSM153168 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153169 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153170 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153171 2 0.1724 0.8587 0.000 0.948 0.020 NA
#> GSM153172 2 0.3257 0.8553 0.000 0.844 0.152 NA
#> GSM153173 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM153174 2 0.2593 0.8653 0.000 0.892 0.104 NA
#> GSM153175 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM153176 2 0.5673 0.2610 0.000 0.596 0.372 NA
#> GSM153177 2 0.4967 0.3408 0.000 0.548 0.452 NA
#> GSM152931 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152932 2 0.3172 0.8525 0.000 0.840 0.160 NA
#> GSM152933 2 0.3494 0.8425 0.000 0.824 0.172 NA
#> GSM152934 2 0.0921 0.8583 0.000 0.972 0.000 NA
#> GSM152935 2 0.4800 0.6009 0.000 0.656 0.340 NA
#> GSM152936 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152937 2 0.4509 0.5288 0.000 0.708 0.288 NA
#> GSM152938 3 0.5000 -0.1589 0.000 0.496 0.504 NA
#> GSM152939 2 0.0592 0.8603 0.000 0.984 0.000 NA
#> GSM152940 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152941 1 0.5404 0.6669 0.512 0.012 0.000 NA
#> GSM152942 2 0.3356 0.8263 0.000 0.824 0.176 NA
#> GSM152943 2 0.0921 0.8583 0.000 0.972 0.000 NA
#> GSM152944 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM152945 2 0.2593 0.8653 0.000 0.892 0.104 NA
#> GSM152946 2 0.3074 0.8564 0.000 0.848 0.152 NA
#> GSM152947 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152948 2 0.3257 0.8553 0.000 0.844 0.152 NA
#> GSM152949 2 0.4916 0.3288 0.000 0.576 0.424 NA
#> GSM152950 2 0.2647 0.8615 0.000 0.880 0.120 NA
#> GSM152951 2 0.1398 0.8678 0.000 0.956 0.040 NA
#> GSM152952 2 0.3157 0.8586 0.000 0.852 0.144 NA
#> GSM152953 2 0.3257 0.8553 0.000 0.844 0.152 NA
#> GSM152954 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152955 2 0.1510 0.8564 0.000 0.956 0.016 NA
#> GSM152956 2 0.3257 0.8553 0.000 0.844 0.152 NA
#> GSM152957 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152958 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152959 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152960 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152961 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152962 2 0.3356 0.8268 0.000 0.824 0.176 NA
#> GSM152963 2 0.3257 0.8553 0.000 0.844 0.152 NA
#> GSM152964 2 0.5543 0.1183 0.000 0.556 0.424 NA
#> GSM152965 2 0.2654 0.8646 0.000 0.888 0.108 NA
#> GSM152966 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152967 2 0.2593 0.8653 0.000 0.892 0.104 NA
#> GSM152968 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM152969 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152970 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152971 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152972 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152973 2 0.2089 0.8589 0.000 0.932 0.048 NA
#> GSM152974 2 0.3219 0.8499 0.000 0.836 0.164 NA
#> GSM152975 2 0.1743 0.8686 0.000 0.940 0.056 NA
#> GSM152976 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152977 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152978 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152979 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM152980 2 0.3013 0.8636 0.000 0.888 0.080 NA
#> GSM152981 3 0.1389 0.8508 0.000 0.048 0.952 NA
#> GSM152982 2 0.0921 0.8583 0.000 0.972 0.000 NA
#> GSM152983 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152984 2 0.0592 0.8603 0.000 0.984 0.000 NA
#> GSM152985 2 0.2797 0.8124 0.068 0.900 0.000 NA
#> GSM152986 2 0.1022 0.8576 0.000 0.968 0.000 NA
#> GSM152987 1 0.2928 0.7065 0.880 0.012 0.000 NA
#> GSM152988 2 0.0707 0.8596 0.000 0.980 0.000 NA
#> GSM152989 2 0.4833 0.6105 0.228 0.740 0.000 NA
#> GSM152990 3 0.0000 0.8956 0.000 0.000 1.000 NA
#> GSM152991 3 0.1389 0.8508 0.000 0.048 0.952 NA
#> GSM187524 1 0.4998 0.6466 0.512 0.000 0.000 NA
#> GSM187525 1 0.4998 0.6466 0.512 0.000 0.000 NA
#> GSM187526 1 0.4992 0.6486 0.524 0.000 0.000 NA
#> GSM187527 1 0.6924 0.6163 0.464 0.108 0.000 NA
#> GSM152856 1 0.4992 0.6733 0.524 0.000 0.000 NA
#> GSM152857 2 0.7469 0.4024 0.068 0.592 0.072 NA
#> GSM152858 1 0.4998 0.6466 0.512 0.000 0.000 NA
#> GSM152859 1 0.4998 0.6466 0.512 0.000 0.000 NA
#> GSM152860 1 0.4998 0.6466 0.512 0.000 0.000 NA
#> GSM152861 1 0.1022 0.7101 0.968 0.000 0.000 NA
#> GSM152862 1 0.4998 0.6466 0.512 0.000 0.000 NA
#> GSM152863 1 0.4888 0.6589 0.588 0.000 0.000 NA
#> GSM152864 1 0.0000 0.7123 1.000 0.000 0.000 NA
#> GSM152865 1 0.0188 0.7121 0.996 0.000 0.000 NA
#> GSM152866 1 0.4992 0.6733 0.524 0.000 0.000 NA
#> GSM152867 1 0.0000 0.7123 1.000 0.000 0.000 NA
#> GSM152868 1 0.0000 0.7123 1.000 0.000 0.000 NA
#> GSM152869 1 0.0000 0.7123 1.000 0.000 0.000 NA
#> GSM152870 1 0.4998 0.6466 0.512 0.000 0.000 NA
#> GSM152871 1 0.4998 0.6466 0.512 0.000 0.000 NA
#> GSM152872 1 0.4998 0.6466 0.512 0.000 0.000 NA
#> GSM152873 1 0.4992 0.6733 0.524 0.000 0.000 NA
#> GSM152874 1 0.4992 0.6733 0.524 0.000 0.000 NA
#> GSM152875 1 0.4992 0.6733 0.524 0.000 0.000 NA
#> GSM152876 1 0.5000 0.6629 0.500 0.000 0.000 NA
#> GSM152877 1 0.4992 0.6733 0.524 0.000 0.000 NA
#> GSM152878 1 0.4996 0.6703 0.516 0.000 0.000 NA
#> GSM152879 1 0.4992 0.6733 0.524 0.000 0.000 NA
#> GSM152880 1 0.4992 0.6733 0.524 0.000 0.000 NA
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.0404 0.905 0.000 0.988 0.012 0.000 0.000
#> GSM152805 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM152806 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM152807 2 0.1364 0.907 0.000 0.952 0.012 0.036 0.000
#> GSM152808 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM152809 2 0.1544 0.896 0.000 0.932 0.000 0.068 0.000
#> GSM152810 3 0.4744 0.547 0.000 0.056 0.692 0.252 0.000
#> GSM152811 3 0.0162 0.953 0.000 0.004 0.996 0.000 0.000
#> GSM152812 2 0.1043 0.904 0.000 0.960 0.000 0.040 0.000
#> GSM152813 2 0.0404 0.905 0.000 0.988 0.012 0.000 0.000
#> GSM152814 2 0.0404 0.905 0.000 0.988 0.012 0.000 0.000
#> GSM152815 2 0.0000 0.904 0.000 1.000 0.000 0.000 0.000
#> GSM152816 3 0.1792 0.895 0.000 0.084 0.916 0.000 0.000
#> GSM152817 3 0.0162 0.954 0.000 0.004 0.996 0.000 0.000
#> GSM152818 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM152819 3 0.1608 0.907 0.000 0.072 0.928 0.000 0.000
#> GSM152820 2 0.1638 0.895 0.000 0.932 0.064 0.004 0.000
#> GSM152821 2 0.0510 0.904 0.000 0.984 0.016 0.000 0.000
#> GSM153115 4 0.1197 0.863 0.000 0.048 0.000 0.952 0.000
#> GSM153116 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153117 3 0.1608 0.907 0.000 0.072 0.928 0.000 0.000
#> GSM153118 2 0.0609 0.904 0.000 0.980 0.020 0.000 0.000
#> GSM153119 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153120 4 0.1197 0.863 0.000 0.048 0.000 0.952 0.000
#> GSM153121 2 0.2852 0.825 0.000 0.828 0.172 0.000 0.000
#> GSM153122 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153123 2 0.0404 0.905 0.000 0.988 0.012 0.000 0.000
#> GSM153124 4 0.2230 0.810 0.000 0.116 0.000 0.884 0.000
#> GSM153125 4 0.1908 0.841 0.000 0.092 0.000 0.908 0.000
#> GSM153126 3 0.0162 0.954 0.000 0.004 0.996 0.000 0.000
#> GSM153127 2 0.1544 0.896 0.000 0.932 0.000 0.068 0.000
#> GSM153128 3 0.1399 0.914 0.000 0.028 0.952 0.020 0.000
#> GSM153129 2 0.2020 0.861 0.000 0.900 0.100 0.000 0.000
#> GSM153130 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153131 2 0.1478 0.893 0.000 0.936 0.064 0.000 0.000
#> GSM153132 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153133 2 0.1704 0.898 0.000 0.928 0.004 0.068 0.000
#> GSM153134 2 0.2127 0.856 0.000 0.892 0.108 0.000 0.000
#> GSM153135 2 0.1544 0.896 0.000 0.932 0.000 0.068 0.000
#> GSM153136 4 0.4242 0.327 0.000 0.428 0.000 0.572 0.000
#> GSM153137 4 0.4182 0.396 0.000 0.400 0.000 0.600 0.000
#> GSM153138 4 0.4331 0.517 0.000 0.400 0.004 0.596 0.000
#> GSM153139 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153140 2 0.0404 0.905 0.000 0.988 0.012 0.000 0.000
#> GSM153141 2 0.1478 0.898 0.000 0.936 0.000 0.064 0.000
#> GSM153142 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153143 2 0.1544 0.896 0.000 0.932 0.000 0.068 0.000
#> GSM153144 2 0.0798 0.907 0.000 0.976 0.016 0.008 0.000
#> GSM153145 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153146 2 0.0510 0.904 0.000 0.984 0.016 0.000 0.000
#> GSM153147 2 0.1704 0.898 0.000 0.928 0.004 0.068 0.000
#> GSM153148 2 0.1544 0.896 0.000 0.932 0.000 0.068 0.000
#> GSM153149 2 0.0771 0.906 0.000 0.976 0.020 0.004 0.000
#> GSM153150 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM153151 2 0.1704 0.898 0.000 0.928 0.004 0.068 0.000
#> GSM153152 2 0.2790 0.890 0.000 0.880 0.052 0.068 0.000
#> GSM153153 2 0.1410 0.895 0.000 0.940 0.060 0.000 0.000
#> GSM153154 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153155 2 0.1544 0.896 0.000 0.932 0.000 0.068 0.000
#> GSM153156 3 0.0162 0.955 0.000 0.004 0.996 0.000 0.000
#> GSM153157 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153158 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153159 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153160 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153161 2 0.1544 0.896 0.000 0.932 0.000 0.068 0.000
#> GSM153162 2 0.1697 0.897 0.000 0.932 0.060 0.008 0.000
#> GSM153163 3 0.0510 0.947 0.000 0.016 0.984 0.000 0.000
#> GSM153164 2 0.1792 0.876 0.000 0.916 0.084 0.000 0.000
#> GSM153165 3 0.1608 0.907 0.000 0.072 0.928 0.000 0.000
#> GSM153166 2 0.2074 0.859 0.000 0.896 0.104 0.000 0.000
#> GSM153167 2 0.1341 0.896 0.000 0.944 0.056 0.000 0.000
#> GSM153168 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153169 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153170 3 0.1608 0.907 0.000 0.072 0.928 0.000 0.000
#> GSM153171 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM153172 2 0.0404 0.905 0.000 0.988 0.012 0.000 0.000
#> GSM153173 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM153174 2 0.1544 0.896 0.000 0.932 0.000 0.068 0.000
#> GSM153175 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM153176 4 0.2520 0.831 0.000 0.056 0.048 0.896 0.000
#> GSM153177 2 0.3242 0.743 0.000 0.784 0.216 0.000 0.000
#> GSM152931 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152932 2 0.1270 0.898 0.000 0.948 0.052 0.000 0.000
#> GSM152933 2 0.0963 0.903 0.000 0.964 0.036 0.000 0.000
#> GSM152934 4 0.3424 0.718 0.000 0.240 0.000 0.760 0.000
#> GSM152935 2 0.1043 0.898 0.000 0.960 0.040 0.000 0.000
#> GSM152936 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152937 2 0.6156 0.177 0.000 0.456 0.412 0.132 0.000
#> GSM152938 2 0.2074 0.859 0.000 0.896 0.104 0.000 0.000
#> GSM152939 2 0.2852 0.800 0.000 0.828 0.000 0.172 0.000
#> GSM152940 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152941 4 0.3707 0.486 0.284 0.000 0.000 0.716 0.000
#> GSM152942 2 0.3527 0.850 0.000 0.828 0.116 0.056 0.000
#> GSM152943 4 0.4273 0.265 0.000 0.448 0.000 0.552 0.000
#> GSM152944 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM152945 2 0.1544 0.896 0.000 0.932 0.000 0.068 0.000
#> GSM152946 2 0.1522 0.896 0.000 0.944 0.012 0.044 0.000
#> GSM152947 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152948 2 0.0324 0.905 0.000 0.992 0.004 0.004 0.000
#> GSM152949 2 0.3621 0.803 0.000 0.788 0.192 0.020 0.000
#> GSM152950 2 0.2719 0.891 0.000 0.884 0.048 0.068 0.000
#> GSM152951 2 0.1608 0.894 0.000 0.928 0.000 0.072 0.000
#> GSM152952 2 0.1478 0.898 0.000 0.936 0.000 0.064 0.000
#> GSM152953 2 0.0162 0.905 0.000 0.996 0.000 0.004 0.000
#> GSM152954 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152955 4 0.3521 0.721 0.000 0.232 0.004 0.764 0.000
#> GSM152956 2 0.1478 0.898 0.000 0.936 0.000 0.064 0.000
#> GSM152957 4 0.1270 0.862 0.000 0.052 0.000 0.948 0.000
#> GSM152958 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152959 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152960 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152961 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152962 2 0.3719 0.848 0.000 0.816 0.116 0.068 0.000
#> GSM152963 2 0.1121 0.903 0.000 0.956 0.000 0.044 0.000
#> GSM152964 3 0.5193 0.286 0.000 0.052 0.584 0.364 0.000
#> GSM152965 2 0.1704 0.898 0.000 0.928 0.004 0.068 0.000
#> GSM152966 4 0.4150 0.429 0.000 0.388 0.000 0.612 0.000
#> GSM152967 2 0.1544 0.896 0.000 0.932 0.000 0.068 0.000
#> GSM152968 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM152969 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152970 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152971 4 0.1341 0.860 0.000 0.056 0.000 0.944 0.000
#> GSM152972 4 0.1270 0.861 0.000 0.052 0.000 0.948 0.000
#> GSM152973 2 0.3424 0.683 0.000 0.760 0.000 0.240 0.000
#> GSM152974 2 0.1270 0.898 0.000 0.948 0.052 0.000 0.000
#> GSM152975 4 0.4273 0.291 0.000 0.448 0.000 0.552 0.000
#> GSM152976 4 0.1197 0.863 0.000 0.048 0.000 0.952 0.000
#> GSM152977 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152978 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152979 3 0.1608 0.907 0.000 0.072 0.928 0.000 0.000
#> GSM152980 4 0.3336 0.754 0.000 0.228 0.000 0.772 0.000
#> GSM152981 3 0.0290 0.950 0.000 0.008 0.992 0.000 0.000
#> GSM152982 4 0.2929 0.773 0.000 0.180 0.000 0.820 0.000
#> GSM152983 4 0.1908 0.843 0.000 0.092 0.000 0.908 0.000
#> GSM152984 2 0.4210 0.264 0.000 0.588 0.000 0.412 0.000
#> GSM152985 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152986 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152987 4 0.5105 0.347 0.264 0.000 0.000 0.660 0.076
#> GSM152988 2 0.3452 0.687 0.000 0.756 0.000 0.244 0.000
#> GSM152989 4 0.1121 0.864 0.000 0.044 0.000 0.956 0.000
#> GSM152990 3 0.1608 0.907 0.000 0.072 0.928 0.000 0.000
#> GSM152991 3 0.0000 0.957 0.000 0.000 1.000 0.000 0.000
#> GSM187524 5 0.0000 0.926 0.000 0.000 0.000 0.000 1.000
#> GSM187525 5 0.0000 0.926 0.000 0.000 0.000 0.000 1.000
#> GSM187526 5 0.0798 0.908 0.016 0.000 0.000 0.008 0.976
#> GSM187527 4 0.3109 0.667 0.200 0.000 0.000 0.800 0.000
#> GSM152856 1 0.0000 0.789 1.000 0.000 0.000 0.000 0.000
#> GSM152857 4 0.6358 0.485 0.300 0.088 0.040 0.572 0.000
#> GSM152858 5 0.0000 0.926 0.000 0.000 0.000 0.000 1.000
#> GSM152859 5 0.0000 0.926 0.000 0.000 0.000 0.000 1.000
#> GSM152860 5 0.0000 0.926 0.000 0.000 0.000 0.000 1.000
#> GSM152861 5 0.5232 -0.240 0.456 0.000 0.000 0.044 0.500
#> GSM152862 5 0.0000 0.926 0.000 0.000 0.000 0.000 1.000
#> GSM152863 5 0.2974 0.796 0.080 0.000 0.000 0.052 0.868
#> GSM152864 1 0.5236 0.232 0.492 0.000 0.000 0.044 0.464
#> GSM152865 1 0.5238 0.207 0.484 0.000 0.000 0.044 0.472
#> GSM152866 1 0.0000 0.789 1.000 0.000 0.000 0.000 0.000
#> GSM152867 1 0.5236 0.232 0.492 0.000 0.000 0.044 0.464
#> GSM152868 1 0.5236 0.232 0.492 0.000 0.000 0.044 0.464
#> GSM152869 1 0.5236 0.232 0.492 0.000 0.000 0.044 0.464
#> GSM152870 5 0.0000 0.926 0.000 0.000 0.000 0.000 1.000
#> GSM152871 5 0.0000 0.926 0.000 0.000 0.000 0.000 1.000
#> GSM152872 5 0.0000 0.926 0.000 0.000 0.000 0.000 1.000
#> GSM152873 1 0.0000 0.789 1.000 0.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.789 1.000 0.000 0.000 0.000 0.000
#> GSM152875 1 0.0000 0.789 1.000 0.000 0.000 0.000 0.000
#> GSM152876 1 0.0000 0.789 1.000 0.000 0.000 0.000 0.000
#> GSM152877 1 0.0000 0.789 1.000 0.000 0.000 0.000 0.000
#> GSM152878 1 0.0000 0.789 1.000 0.000 0.000 0.000 0.000
#> GSM152879 1 0.0000 0.789 1.000 0.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.789 1.000 0.000 0.000 0.000 0.000
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.0363 0.8533 0.000 0.988 0.000 0.000 0.000 0.012
#> GSM152805 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152806 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152807 2 0.1594 0.8579 0.000 0.932 0.000 0.052 0.000 0.016
#> GSM152808 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152809 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM152810 5 0.3863 0.5761 0.000 0.028 0.000 0.260 0.712 0.000
#> GSM152811 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152812 2 0.1204 0.8538 0.000 0.944 0.000 0.056 0.000 0.000
#> GSM152813 2 0.2454 0.8508 0.000 0.840 0.000 0.000 0.000 0.160
#> GSM152814 2 0.2454 0.8508 0.000 0.840 0.000 0.000 0.000 0.160
#> GSM152815 2 0.0000 0.8531 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152816 5 0.4026 0.7071 0.000 0.088 0.000 0.000 0.752 0.160
#> GSM152817 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152818 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152819 5 0.4026 0.7071 0.000 0.088 0.000 0.000 0.752 0.160
#> GSM152820 2 0.3203 0.8461 0.000 0.812 0.000 0.004 0.024 0.160
#> GSM152821 2 0.1204 0.8572 0.000 0.944 0.000 0.000 0.000 0.056
#> GSM153115 4 0.0146 0.8465 0.000 0.004 0.000 0.996 0.000 0.000
#> GSM153116 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153117 5 0.2019 0.8324 0.000 0.088 0.000 0.000 0.900 0.012
#> GSM153118 2 0.2595 0.8504 0.000 0.836 0.000 0.000 0.004 0.160
#> GSM153119 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153120 4 0.0146 0.8462 0.000 0.004 0.000 0.996 0.000 0.000
#> GSM153121 2 0.3791 0.7296 0.000 0.732 0.000 0.000 0.236 0.032
#> GSM153122 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153123 2 0.2454 0.8508 0.000 0.840 0.000 0.000 0.000 0.160
#> GSM153124 4 0.1714 0.7671 0.000 0.092 0.000 0.908 0.000 0.000
#> GSM153125 4 0.1141 0.8223 0.000 0.052 0.000 0.948 0.000 0.000
#> GSM153126 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153127 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM153128 5 0.1498 0.8527 0.000 0.028 0.000 0.032 0.940 0.000
#> GSM153129 2 0.2981 0.8454 0.000 0.820 0.000 0.000 0.020 0.160
#> GSM153130 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153131 2 0.3062 0.8434 0.000 0.816 0.000 0.000 0.024 0.160
#> GSM153132 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153133 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM153134 2 0.3062 0.8434 0.000 0.816 0.000 0.000 0.024 0.160
#> GSM153135 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM153136 4 0.3756 0.2991 0.000 0.400 0.000 0.600 0.000 0.000
#> GSM153137 4 0.3684 0.3683 0.000 0.372 0.000 0.628 0.000 0.000
#> GSM153138 4 0.3998 0.2806 0.000 0.492 0.000 0.504 0.000 0.004
#> GSM153139 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153140 2 0.2454 0.8508 0.000 0.840 0.000 0.000 0.000 0.160
#> GSM153141 2 0.1556 0.8492 0.000 0.920 0.000 0.080 0.000 0.000
#> GSM153142 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153143 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM153144 2 0.2398 0.8667 0.000 0.876 0.000 0.020 0.000 0.104
#> GSM153145 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153146 2 0.0713 0.8525 0.000 0.972 0.000 0.000 0.000 0.028
#> GSM153147 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM153148 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM153149 2 0.1296 0.8579 0.000 0.948 0.000 0.004 0.004 0.044
#> GSM153150 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153151 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM153152 2 0.4365 0.8479 0.000 0.756 0.000 0.088 0.024 0.132
#> GSM153153 2 0.2981 0.8453 0.000 0.820 0.000 0.000 0.020 0.160
#> GSM153154 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153155 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM153156 5 0.1957 0.8254 0.000 0.000 0.000 0.000 0.888 0.112
#> GSM153157 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153158 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153159 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153160 5 0.0363 0.8949 0.000 0.000 0.000 0.000 0.988 0.012
#> GSM153161 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM153162 2 0.3331 0.8487 0.000 0.808 0.000 0.012 0.020 0.160
#> GSM153163 5 0.1176 0.8763 0.000 0.020 0.000 0.000 0.956 0.024
#> GSM153164 2 0.2896 0.8470 0.000 0.824 0.000 0.000 0.016 0.160
#> GSM153165 5 0.4026 0.7071 0.000 0.088 0.000 0.000 0.752 0.160
#> GSM153166 2 0.3062 0.8434 0.000 0.816 0.000 0.000 0.024 0.160
#> GSM153167 2 0.2896 0.8470 0.000 0.824 0.000 0.000 0.016 0.160
#> GSM153168 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153169 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153170 5 0.4026 0.7071 0.000 0.088 0.000 0.000 0.752 0.160
#> GSM153171 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153172 2 0.1714 0.8587 0.000 0.908 0.000 0.000 0.000 0.092
#> GSM153173 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153174 2 0.3602 0.8556 0.000 0.796 0.000 0.088 0.000 0.116
#> GSM153175 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM153176 4 0.1434 0.8135 0.000 0.012 0.000 0.940 0.048 0.000
#> GSM153177 2 0.3351 0.8335 0.000 0.800 0.000 0.000 0.040 0.160
#> GSM152931 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152932 2 0.2896 0.8470 0.000 0.824 0.000 0.000 0.016 0.160
#> GSM152933 2 0.2706 0.8495 0.000 0.832 0.000 0.000 0.008 0.160
#> GSM152934 4 0.2854 0.6884 0.000 0.208 0.000 0.792 0.000 0.000
#> GSM152935 2 0.2454 0.8508 0.000 0.840 0.000 0.000 0.000 0.160
#> GSM152936 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152937 5 0.5970 -0.0662 0.000 0.380 0.000 0.224 0.396 0.000
#> GSM152938 2 0.3062 0.8434 0.000 0.816 0.000 0.000 0.024 0.160
#> GSM152939 2 0.3101 0.7276 0.000 0.756 0.000 0.244 0.000 0.000
#> GSM152940 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152941 4 0.4198 0.5363 0.000 0.000 0.232 0.708 0.000 0.060
#> GSM152942 2 0.5111 0.8152 0.000 0.708 0.000 0.076 0.084 0.132
#> GSM152943 4 0.3756 0.2788 0.000 0.400 0.000 0.600 0.000 0.000
#> GSM152944 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152945 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM152946 2 0.2981 0.8478 0.000 0.820 0.000 0.020 0.000 0.160
#> GSM152947 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152948 2 0.0405 0.8544 0.000 0.988 0.000 0.004 0.000 0.008
#> GSM152949 2 0.4931 0.8012 0.000 0.700 0.000 0.024 0.120 0.156
#> GSM152950 2 0.4286 0.8491 0.000 0.760 0.000 0.088 0.020 0.132
#> GSM152951 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM152952 2 0.1556 0.8492 0.000 0.920 0.000 0.080 0.000 0.000
#> GSM152953 2 0.0363 0.8549 0.000 0.988 0.000 0.012 0.000 0.000
#> GSM152954 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152955 4 0.3023 0.6775 0.000 0.212 0.000 0.784 0.004 0.000
#> GSM152956 2 0.1556 0.8492 0.000 0.920 0.000 0.080 0.000 0.000
#> GSM152957 4 0.0260 0.8449 0.000 0.008 0.000 0.992 0.000 0.000
#> GSM152958 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152959 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152960 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152961 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152962 2 0.5254 0.8137 0.000 0.696 0.000 0.088 0.084 0.132
#> GSM152963 2 0.1267 0.8533 0.000 0.940 0.000 0.060 0.000 0.000
#> GSM152964 5 0.4371 0.3186 0.000 0.028 0.000 0.392 0.580 0.000
#> GSM152965 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM152966 4 0.3647 0.4044 0.000 0.360 0.000 0.640 0.000 0.000
#> GSM152967 2 0.1663 0.8469 0.000 0.912 0.000 0.088 0.000 0.000
#> GSM152968 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152969 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152970 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152971 4 0.0713 0.8347 0.000 0.028 0.000 0.972 0.000 0.000
#> GSM152972 4 0.0363 0.8428 0.000 0.012 0.000 0.988 0.000 0.000
#> GSM152973 2 0.3175 0.7172 0.000 0.744 0.000 0.256 0.000 0.000
#> GSM152974 2 0.2896 0.8470 0.000 0.824 0.000 0.000 0.016 0.160
#> GSM152975 4 0.4514 0.3795 0.000 0.372 0.000 0.588 0.000 0.040
#> GSM152976 4 0.0146 0.8465 0.000 0.004 0.000 0.996 0.000 0.000
#> GSM152977 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152978 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152979 5 0.4026 0.7071 0.000 0.088 0.000 0.000 0.752 0.160
#> GSM152980 4 0.3499 0.5920 0.000 0.320 0.000 0.680 0.000 0.000
#> GSM152981 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152982 4 0.2340 0.7451 0.000 0.148 0.000 0.852 0.000 0.000
#> GSM152983 4 0.1327 0.8170 0.000 0.064 0.000 0.936 0.000 0.000
#> GSM152984 2 0.3851 0.2184 0.000 0.540 0.000 0.460 0.000 0.000
#> GSM152985 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152986 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152987 4 0.6182 0.1454 0.060 0.000 0.112 0.536 0.000 0.292
#> GSM152988 2 0.3198 0.7047 0.000 0.740 0.000 0.260 0.000 0.000
#> GSM152989 4 0.0000 0.8474 0.000 0.000 0.000 1.000 0.000 0.000
#> GSM152990 5 0.4026 0.7071 0.000 0.088 0.000 0.000 0.752 0.160
#> GSM152991 5 0.0000 0.9012 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM187524 1 0.0000 0.9566 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM187525 1 0.0260 0.9494 0.992 0.000 0.000 0.000 0.000 0.008
#> GSM187526 1 0.4567 0.5263 0.712 0.000 0.004 0.144 0.000 0.140
#> GSM187527 4 0.2597 0.6983 0.000 0.000 0.176 0.824 0.000 0.000
#> GSM152856 3 0.0000 1.0000 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM152857 4 0.6506 0.4192 0.000 0.040 0.180 0.572 0.028 0.180
#> GSM152858 1 0.0000 0.9566 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152859 1 0.0000 0.9566 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152860 1 0.0000 0.9566 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152861 6 0.2558 0.9657 0.156 0.000 0.004 0.000 0.000 0.840
#> GSM152862 1 0.0000 0.9566 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152863 6 0.2790 0.9865 0.140 0.000 0.020 0.000 0.000 0.840
#> GSM152864 6 0.2868 0.9908 0.132 0.000 0.028 0.000 0.000 0.840
#> GSM152865 6 0.2831 0.9896 0.136 0.000 0.024 0.000 0.000 0.840
#> GSM152866 3 0.0000 1.0000 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM152867 6 0.2868 0.9908 0.132 0.000 0.028 0.000 0.000 0.840
#> GSM152868 6 0.2868 0.9908 0.132 0.000 0.028 0.000 0.000 0.840
#> GSM152869 6 0.2868 0.9908 0.132 0.000 0.028 0.000 0.000 0.840
#> GSM152870 1 0.0000 0.9566 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152871 1 0.0000 0.9566 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152872 1 0.0000 0.9566 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152873 3 0.0000 1.0000 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM152874 3 0.0000 1.0000 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM152875 3 0.0000 1.0000 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM152876 3 0.0000 1.0000 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM152877 3 0.0000 1.0000 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM152878 3 0.0000 1.0000 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM152879 3 0.0000 1.0000 0.000 0.000 1.000 0.000 0.000 0.000
#> GSM152880 3 0.0000 1.0000 0.000 0.000 1.000 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> ATC:pam 170 3.94e-28 2
#> ATC:pam 160 4.46e-28 3
#> ATC:pam 159 3.65e-28 4
#> ATC:pam 154 2.80e-29 5
#> ATC:pam 160 1.41e-30 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "mclust"]
# you can also extract it by
# res = res_list["ATC:mclust"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'mclust' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.993 0.997 0.2875 0.717 0.717
#> 3 3 0.887 0.908 0.955 1.1031 0.678 0.551
#> 4 4 0.714 0.787 0.814 0.1712 0.774 0.488
#> 5 5 0.790 0.823 0.896 0.0334 0.900 0.688
#> 6 6 0.737 0.787 0.865 0.0878 0.896 0.631
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.000 0.997 0.000 1.000
#> GSM152805 2 0.000 0.997 0.000 1.000
#> GSM152806 2 0.000 0.997 0.000 1.000
#> GSM152807 2 0.000 0.997 0.000 1.000
#> GSM152808 2 0.000 0.997 0.000 1.000
#> GSM152809 2 0.000 0.997 0.000 1.000
#> GSM152810 2 0.000 0.997 0.000 1.000
#> GSM152811 2 0.000 0.997 0.000 1.000
#> GSM152812 2 0.000 0.997 0.000 1.000
#> GSM152813 2 0.000 0.997 0.000 1.000
#> GSM152814 2 0.000 0.997 0.000 1.000
#> GSM152815 2 0.000 0.997 0.000 1.000
#> GSM152816 2 0.000 0.997 0.000 1.000
#> GSM152817 2 0.000 0.997 0.000 1.000
#> GSM152818 2 0.000 0.997 0.000 1.000
#> GSM152819 2 0.000 0.997 0.000 1.000
#> GSM152820 2 0.000 0.997 0.000 1.000
#> GSM152821 2 0.000 0.997 0.000 1.000
#> GSM153115 2 0.000 0.997 0.000 1.000
#> GSM153116 2 0.000 0.997 0.000 1.000
#> GSM153117 2 0.000 0.997 0.000 1.000
#> GSM153118 2 0.000 0.997 0.000 1.000
#> GSM153119 2 0.000 0.997 0.000 1.000
#> GSM153120 2 0.000 0.997 0.000 1.000
#> GSM153121 2 0.000 0.997 0.000 1.000
#> GSM153122 2 0.000 0.997 0.000 1.000
#> GSM153123 2 0.000 0.997 0.000 1.000
#> GSM153124 2 0.000 0.997 0.000 1.000
#> GSM153125 2 0.000 0.997 0.000 1.000
#> GSM153126 2 0.000 0.997 0.000 1.000
#> GSM153127 2 0.000 0.997 0.000 1.000
#> GSM153128 2 0.000 0.997 0.000 1.000
#> GSM153129 2 0.000 0.997 0.000 1.000
#> GSM153130 2 0.000 0.997 0.000 1.000
#> GSM153131 2 0.000 0.997 0.000 1.000
#> GSM153132 2 0.000 0.997 0.000 1.000
#> GSM153133 2 0.000 0.997 0.000 1.000
#> GSM153134 2 0.000 0.997 0.000 1.000
#> GSM153135 2 0.000 0.997 0.000 1.000
#> GSM153136 2 0.000 0.997 0.000 1.000
#> GSM153137 2 0.000 0.997 0.000 1.000
#> GSM153138 2 0.000 0.997 0.000 1.000
#> GSM153139 2 0.000 0.997 0.000 1.000
#> GSM153140 2 0.000 0.997 0.000 1.000
#> GSM153141 2 0.000 0.997 0.000 1.000
#> GSM153142 2 0.000 0.997 0.000 1.000
#> GSM153143 2 0.000 0.997 0.000 1.000
#> GSM153144 2 0.000 0.997 0.000 1.000
#> GSM153145 2 0.000 0.997 0.000 1.000
#> GSM153146 2 0.000 0.997 0.000 1.000
#> GSM153147 2 0.000 0.997 0.000 1.000
#> GSM153148 2 0.000 0.997 0.000 1.000
#> GSM153149 2 0.000 0.997 0.000 1.000
#> GSM153150 2 0.000 0.997 0.000 1.000
#> GSM153151 2 0.000 0.997 0.000 1.000
#> GSM153152 2 0.000 0.997 0.000 1.000
#> GSM153153 2 0.000 0.997 0.000 1.000
#> GSM153154 2 0.000 0.997 0.000 1.000
#> GSM153155 2 0.000 0.997 0.000 1.000
#> GSM153156 2 0.000 0.997 0.000 1.000
#> GSM153157 2 0.000 0.997 0.000 1.000
#> GSM153158 2 0.000 0.997 0.000 1.000
#> GSM153159 2 0.000 0.997 0.000 1.000
#> GSM153160 2 0.000 0.997 0.000 1.000
#> GSM153161 2 0.000 0.997 0.000 1.000
#> GSM153162 2 0.000 0.997 0.000 1.000
#> GSM153163 2 0.000 0.997 0.000 1.000
#> GSM153164 2 0.000 0.997 0.000 1.000
#> GSM153165 2 0.000 0.997 0.000 1.000
#> GSM153166 2 0.000 0.997 0.000 1.000
#> GSM153167 2 0.000 0.997 0.000 1.000
#> GSM153168 2 0.000 0.997 0.000 1.000
#> GSM153169 2 0.000 0.997 0.000 1.000
#> GSM153170 2 0.000 0.997 0.000 1.000
#> GSM153171 2 0.000 0.997 0.000 1.000
#> GSM153172 2 0.000 0.997 0.000 1.000
#> GSM153173 2 0.000 0.997 0.000 1.000
#> GSM153174 2 0.000 0.997 0.000 1.000
#> GSM153175 2 0.000 0.997 0.000 1.000
#> GSM153176 2 0.000 0.997 0.000 1.000
#> GSM153177 2 0.000 0.997 0.000 1.000
#> GSM152931 2 0.000 0.997 0.000 1.000
#> GSM152932 2 0.000 0.997 0.000 1.000
#> GSM152933 2 0.000 0.997 0.000 1.000
#> GSM152934 2 0.000 0.997 0.000 1.000
#> GSM152935 2 0.000 0.997 0.000 1.000
#> GSM152936 2 0.000 0.997 0.000 1.000
#> GSM152937 2 0.000 0.997 0.000 1.000
#> GSM152938 2 0.000 0.997 0.000 1.000
#> GSM152939 2 0.000 0.997 0.000 1.000
#> GSM152940 2 0.000 0.997 0.000 1.000
#> GSM152941 2 0.224 0.960 0.036 0.964
#> GSM152942 2 0.000 0.997 0.000 1.000
#> GSM152943 2 0.000 0.997 0.000 1.000
#> GSM152944 2 0.000 0.997 0.000 1.000
#> GSM152945 2 0.000 0.997 0.000 1.000
#> GSM152946 2 0.000 0.997 0.000 1.000
#> GSM152947 2 0.000 0.997 0.000 1.000
#> GSM152948 2 0.000 0.997 0.000 1.000
#> GSM152949 2 0.000 0.997 0.000 1.000
#> GSM152950 2 0.000 0.997 0.000 1.000
#> GSM152951 2 0.000 0.997 0.000 1.000
#> GSM152952 2 0.000 0.997 0.000 1.000
#> GSM152953 2 0.000 0.997 0.000 1.000
#> GSM152954 2 0.000 0.997 0.000 1.000
#> GSM152955 2 0.000 0.997 0.000 1.000
#> GSM152956 2 0.000 0.997 0.000 1.000
#> GSM152957 2 0.000 0.997 0.000 1.000
#> GSM152958 2 0.000 0.997 0.000 1.000
#> GSM152959 2 0.000 0.997 0.000 1.000
#> GSM152960 2 0.000 0.997 0.000 1.000
#> GSM152961 2 0.000 0.997 0.000 1.000
#> GSM152962 2 0.000 0.997 0.000 1.000
#> GSM152963 2 0.000 0.997 0.000 1.000
#> GSM152964 2 0.000 0.997 0.000 1.000
#> GSM152965 2 0.000 0.997 0.000 1.000
#> GSM152966 2 0.000 0.997 0.000 1.000
#> GSM152967 2 0.000 0.997 0.000 1.000
#> GSM152968 2 0.000 0.997 0.000 1.000
#> GSM152969 2 0.000 0.997 0.000 1.000
#> GSM152970 2 0.000 0.997 0.000 1.000
#> GSM152971 2 0.000 0.997 0.000 1.000
#> GSM152972 2 0.000 0.997 0.000 1.000
#> GSM152973 2 0.000 0.997 0.000 1.000
#> GSM152974 2 0.000 0.997 0.000 1.000
#> GSM152975 2 0.000 0.997 0.000 1.000
#> GSM152976 2 0.000 0.997 0.000 1.000
#> GSM152977 2 0.000 0.997 0.000 1.000
#> GSM152978 2 0.000 0.997 0.000 1.000
#> GSM152979 2 0.000 0.997 0.000 1.000
#> GSM152980 2 0.000 0.997 0.000 1.000
#> GSM152981 2 0.000 0.997 0.000 1.000
#> GSM152982 2 0.000 0.997 0.000 1.000
#> GSM152983 2 0.000 0.997 0.000 1.000
#> GSM152984 2 0.000 0.997 0.000 1.000
#> GSM152985 2 0.000 0.997 0.000 1.000
#> GSM152986 2 0.000 0.997 0.000 1.000
#> GSM152987 2 0.980 0.289 0.416 0.584
#> GSM152988 2 0.000 0.997 0.000 1.000
#> GSM152989 2 0.000 0.997 0.000 1.000
#> GSM152990 2 0.000 0.997 0.000 1.000
#> GSM152991 2 0.000 0.997 0.000 1.000
#> GSM187524 1 0.000 1.000 1.000 0.000
#> GSM187525 1 0.000 1.000 1.000 0.000
#> GSM187526 1 0.000 1.000 1.000 0.000
#> GSM187527 1 0.000 1.000 1.000 0.000
#> GSM152856 1 0.000 1.000 1.000 0.000
#> GSM152857 1 0.000 1.000 1.000 0.000
#> GSM152858 1 0.000 1.000 1.000 0.000
#> GSM152859 1 0.000 1.000 1.000 0.000
#> GSM152860 1 0.000 1.000 1.000 0.000
#> GSM152861 1 0.000 1.000 1.000 0.000
#> GSM152862 1 0.000 1.000 1.000 0.000
#> GSM152863 1 0.000 1.000 1.000 0.000
#> GSM152864 1 0.000 1.000 1.000 0.000
#> GSM152865 1 0.000 1.000 1.000 0.000
#> GSM152866 1 0.000 1.000 1.000 0.000
#> GSM152867 1 0.000 1.000 1.000 0.000
#> GSM152868 1 0.000 1.000 1.000 0.000
#> GSM152869 1 0.000 1.000 1.000 0.000
#> GSM152870 1 0.000 1.000 1.000 0.000
#> GSM152871 1 0.000 1.000 1.000 0.000
#> GSM152872 1 0.000 1.000 1.000 0.000
#> GSM152873 1 0.000 1.000 1.000 0.000
#> GSM152874 1 0.000 1.000 1.000 0.000
#> GSM152875 1 0.000 1.000 1.000 0.000
#> GSM152876 1 0.000 1.000 1.000 0.000
#> GSM152877 1 0.000 1.000 1.000 0.000
#> GSM152878 1 0.000 1.000 1.000 0.000
#> GSM152879 1 0.000 1.000 1.000 0.000
#> GSM152880 1 0.000 1.000 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.0747 0.933 0.000 0.984 0.016
#> GSM152805 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152806 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152807 2 0.2165 0.889 0.000 0.936 0.064
#> GSM152808 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152809 3 0.6280 0.227 0.000 0.460 0.540
#> GSM152810 3 0.4178 0.786 0.000 0.172 0.828
#> GSM152811 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152812 3 0.5859 0.547 0.000 0.344 0.656
#> GSM152813 2 0.3752 0.801 0.000 0.856 0.144
#> GSM152814 2 0.3816 0.796 0.000 0.852 0.148
#> GSM152815 2 0.0592 0.936 0.000 0.988 0.012
#> GSM152816 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152817 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152818 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152819 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152820 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152821 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153115 2 0.0000 0.941 0.000 1.000 0.000
#> GSM153116 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153117 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153118 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153119 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153120 2 0.0000 0.941 0.000 1.000 0.000
#> GSM153121 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153122 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153123 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153124 2 0.0000 0.941 0.000 1.000 0.000
#> GSM153125 2 0.0000 0.941 0.000 1.000 0.000
#> GSM153126 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153127 3 0.3116 0.899 0.000 0.108 0.892
#> GSM153128 3 0.0592 0.931 0.000 0.012 0.988
#> GSM153129 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153130 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153131 3 0.0592 0.935 0.000 0.012 0.988
#> GSM153132 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153133 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153134 3 0.0424 0.935 0.000 0.008 0.992
#> GSM153135 3 0.5397 0.676 0.000 0.280 0.720
#> GSM153136 2 0.0000 0.941 0.000 1.000 0.000
#> GSM153137 2 0.6168 0.227 0.000 0.588 0.412
#> GSM153138 2 0.6204 0.232 0.000 0.576 0.424
#> GSM153139 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153140 2 0.3412 0.825 0.000 0.876 0.124
#> GSM153141 2 0.5706 0.488 0.000 0.680 0.320
#> GSM153142 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153143 3 0.2537 0.920 0.000 0.080 0.920
#> GSM153144 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153145 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153146 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153147 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153148 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153149 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153150 2 0.0000 0.941 0.000 1.000 0.000
#> GSM153151 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153152 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153153 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153154 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153155 3 0.2625 0.918 0.000 0.084 0.916
#> GSM153156 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153157 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153158 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153159 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153160 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153161 3 0.3412 0.885 0.000 0.124 0.876
#> GSM153162 3 0.0747 0.934 0.000 0.016 0.984
#> GSM153163 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153164 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153165 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153166 3 0.2165 0.925 0.000 0.064 0.936
#> GSM153167 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153168 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153169 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153170 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153171 2 0.0000 0.941 0.000 1.000 0.000
#> GSM153172 3 0.2625 0.918 0.000 0.084 0.916
#> GSM153173 3 0.0000 0.935 0.000 0.000 1.000
#> GSM153174 3 0.2448 0.922 0.000 0.076 0.924
#> GSM153175 2 0.0000 0.941 0.000 1.000 0.000
#> GSM153176 3 0.5327 0.685 0.000 0.272 0.728
#> GSM153177 3 0.1860 0.928 0.000 0.052 0.948
#> GSM152931 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152932 3 0.2625 0.917 0.000 0.084 0.916
#> GSM152933 3 0.2448 0.922 0.000 0.076 0.924
#> GSM152934 2 0.1163 0.921 0.000 0.972 0.028
#> GSM152935 3 0.2448 0.922 0.000 0.076 0.924
#> GSM152936 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152937 3 0.1529 0.919 0.000 0.040 0.960
#> GSM152938 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152939 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152940 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152941 2 0.0237 0.939 0.004 0.996 0.000
#> GSM152942 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152943 2 0.1860 0.902 0.000 0.948 0.052
#> GSM152944 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152945 3 0.2537 0.920 0.000 0.080 0.920
#> GSM152946 2 0.0592 0.936 0.000 0.988 0.012
#> GSM152947 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152948 2 0.0747 0.933 0.000 0.984 0.016
#> GSM152949 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152950 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152951 2 0.0592 0.936 0.000 0.988 0.012
#> GSM152952 3 0.4002 0.849 0.000 0.160 0.840
#> GSM152953 3 0.4062 0.844 0.000 0.164 0.836
#> GSM152954 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152955 3 0.3192 0.898 0.000 0.112 0.888
#> GSM152956 3 0.3192 0.896 0.000 0.112 0.888
#> GSM152957 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152958 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152959 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152960 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152961 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152962 3 0.0237 0.935 0.000 0.004 0.996
#> GSM152963 3 0.2537 0.920 0.000 0.080 0.920
#> GSM152964 3 0.4291 0.775 0.000 0.180 0.820
#> GSM152965 3 0.2448 0.922 0.000 0.076 0.924
#> GSM152966 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152967 3 0.5835 0.561 0.000 0.340 0.660
#> GSM152968 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152969 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152970 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152971 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152972 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152973 3 0.6095 0.453 0.000 0.392 0.608
#> GSM152974 3 0.2448 0.922 0.000 0.076 0.924
#> GSM152975 2 0.0892 0.930 0.000 0.980 0.020
#> GSM152976 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152977 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152978 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152979 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152980 2 0.1411 0.917 0.000 0.964 0.036
#> GSM152981 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152982 2 0.0592 0.935 0.000 0.988 0.012
#> GSM152983 2 0.0237 0.940 0.000 0.996 0.004
#> GSM152984 2 0.6204 0.182 0.000 0.576 0.424
#> GSM152985 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152986 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152987 2 0.0592 0.932 0.012 0.988 0.000
#> GSM152988 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152989 2 0.0000 0.941 0.000 1.000 0.000
#> GSM152990 3 0.0000 0.935 0.000 0.000 1.000
#> GSM152991 3 0.0000 0.935 0.000 0.000 1.000
#> GSM187524 1 0.0000 0.999 1.000 0.000 0.000
#> GSM187525 1 0.0000 0.999 1.000 0.000 0.000
#> GSM187526 1 0.0000 0.999 1.000 0.000 0.000
#> GSM187527 1 0.1411 0.960 0.964 0.036 0.000
#> GSM152856 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152857 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152858 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152859 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152860 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152861 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152862 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152863 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152864 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152865 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152866 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152867 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152868 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152869 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152870 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152871 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152872 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152873 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152874 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152875 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152876 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152877 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152878 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152879 1 0.0000 0.999 1.000 0.000 0.000
#> GSM152880 1 0.0000 0.999 1.000 0.000 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.4454 0.510 0.000 0.692 0.000 0.308
#> GSM152805 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM152806 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM152807 2 0.4406 0.524 0.000 0.700 0.000 0.300
#> GSM152808 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM152809 2 0.1389 0.826 0.000 0.952 0.000 0.048
#> GSM152810 3 0.5770 -0.300 0.020 0.008 0.580 0.392
#> GSM152811 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM152812 2 0.1302 0.829 0.000 0.956 0.000 0.044
#> GSM152813 2 0.4331 0.544 0.000 0.712 0.000 0.288
#> GSM152814 2 0.4304 0.551 0.000 0.716 0.000 0.284
#> GSM152815 2 0.4406 0.524 0.000 0.700 0.000 0.300
#> GSM152816 3 0.4535 0.897 0.000 0.292 0.704 0.004
#> GSM152817 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM152818 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM152819 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM152820 2 0.4543 0.174 0.000 0.676 0.324 0.000
#> GSM152821 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153115 4 0.1302 0.881 0.000 0.044 0.000 0.956
#> GSM153116 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153117 2 0.2921 0.673 0.000 0.860 0.140 0.000
#> GSM153118 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153119 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153120 4 0.4370 0.860 0.000 0.044 0.156 0.800
#> GSM153121 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153122 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153123 2 0.0188 0.847 0.000 0.996 0.000 0.004
#> GSM153124 4 0.2149 0.861 0.000 0.088 0.000 0.912
#> GSM153125 4 0.1302 0.881 0.000 0.044 0.000 0.956
#> GSM153126 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153127 2 0.0469 0.845 0.000 0.988 0.000 0.012
#> GSM153128 3 0.5237 -0.183 0.000 0.016 0.628 0.356
#> GSM153129 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153130 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153131 3 0.5269 0.786 0.000 0.364 0.620 0.016
#> GSM153132 2 0.4522 0.206 0.000 0.680 0.320 0.000
#> GSM153133 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153134 2 0.1452 0.830 0.000 0.956 0.008 0.036
#> GSM153135 2 0.1118 0.834 0.000 0.964 0.000 0.036
#> GSM153136 4 0.1302 0.881 0.000 0.044 0.000 0.956
#> GSM153137 4 0.5613 0.807 0.000 0.120 0.156 0.724
#> GSM153138 2 0.4898 0.658 0.000 0.780 0.104 0.116
#> GSM153139 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153140 2 0.4406 0.524 0.000 0.700 0.000 0.300
#> GSM153141 2 0.2011 0.799 0.000 0.920 0.000 0.080
#> GSM153142 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153143 2 0.0592 0.844 0.000 0.984 0.000 0.016
#> GSM153144 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153145 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153146 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153147 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153148 2 0.0188 0.846 0.000 0.996 0.000 0.004
#> GSM153149 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153150 4 0.4370 0.860 0.000 0.044 0.156 0.800
#> GSM153151 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153152 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153153 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153154 2 0.4992 -0.434 0.000 0.524 0.476 0.000
#> GSM153155 2 0.0469 0.845 0.000 0.988 0.000 0.012
#> GSM153156 3 0.4643 0.832 0.000 0.344 0.656 0.000
#> GSM153157 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153158 3 0.4406 0.897 0.000 0.300 0.700 0.000
#> GSM153159 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153160 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153161 2 0.0707 0.842 0.000 0.980 0.000 0.020
#> GSM153162 2 0.0336 0.841 0.000 0.992 0.008 0.000
#> GSM153163 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153164 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153165 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153166 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153167 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153168 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153169 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153170 2 0.4605 0.139 0.000 0.664 0.336 0.000
#> GSM153171 4 0.1302 0.881 0.000 0.044 0.000 0.956
#> GSM153172 2 0.0188 0.846 0.000 0.996 0.000 0.004
#> GSM153173 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM153174 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM153175 4 0.1302 0.881 0.000 0.044 0.000 0.956
#> GSM153176 4 0.5183 0.413 0.008 0.000 0.408 0.584
#> GSM153177 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM152931 4 0.1302 0.881 0.000 0.044 0.000 0.956
#> GSM152932 2 0.0188 0.847 0.000 0.996 0.000 0.004
#> GSM152933 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM152934 4 0.4417 0.859 0.000 0.044 0.160 0.796
#> GSM152935 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM152936 4 0.4370 0.860 0.000 0.044 0.156 0.800
#> GSM152937 3 0.5364 -0.274 0.000 0.016 0.592 0.392
#> GSM152938 2 0.4866 -0.180 0.000 0.596 0.404 0.000
#> GSM152939 4 0.1302 0.881 0.000 0.044 0.000 0.956
#> GSM152940 4 0.4370 0.860 0.000 0.044 0.156 0.800
#> GSM152941 1 0.5461 0.623 0.696 0.012 0.028 0.264
#> GSM152942 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM152943 4 0.5204 0.843 0.000 0.088 0.160 0.752
#> GSM152944 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM152945 2 0.0188 0.846 0.000 0.996 0.000 0.004
#> GSM152946 2 0.4431 0.517 0.000 0.696 0.000 0.304
#> GSM152947 4 0.1302 0.881 0.000 0.044 0.000 0.956
#> GSM152948 2 0.4406 0.524 0.000 0.700 0.000 0.300
#> GSM152949 2 0.4331 0.305 0.000 0.712 0.288 0.000
#> GSM152950 2 0.2530 0.711 0.000 0.888 0.112 0.000
#> GSM152951 2 0.4331 0.545 0.000 0.712 0.000 0.288
#> GSM152952 2 0.1820 0.822 0.000 0.944 0.020 0.036
#> GSM152953 2 0.1118 0.834 0.000 0.964 0.000 0.036
#> GSM152954 4 0.4370 0.860 0.000 0.044 0.156 0.800
#> GSM152955 2 0.0779 0.841 0.000 0.980 0.004 0.016
#> GSM152956 2 0.0707 0.842 0.000 0.980 0.000 0.020
#> GSM152957 4 0.1888 0.878 0.000 0.044 0.016 0.940
#> GSM152958 4 0.4174 0.865 0.000 0.044 0.140 0.816
#> GSM152959 4 0.4370 0.860 0.000 0.044 0.156 0.800
#> GSM152960 4 0.4417 0.859 0.000 0.044 0.160 0.796
#> GSM152961 4 0.1489 0.880 0.000 0.044 0.004 0.952
#> GSM152962 2 0.0188 0.843 0.000 0.996 0.004 0.000
#> GSM152963 2 0.0188 0.846 0.000 0.996 0.000 0.004
#> GSM152964 3 0.5456 -0.295 0.008 0.008 0.588 0.396
#> GSM152965 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM152966 4 0.1302 0.881 0.000 0.044 0.000 0.956
#> GSM152967 2 0.1716 0.813 0.000 0.936 0.000 0.064
#> GSM152968 2 0.3569 0.557 0.000 0.804 0.196 0.000
#> GSM152969 4 0.1302 0.881 0.000 0.044 0.000 0.956
#> GSM152970 4 0.1888 0.878 0.000 0.044 0.016 0.940
#> GSM152971 4 0.1302 0.881 0.000 0.044 0.000 0.956
#> GSM152972 4 0.4017 0.868 0.000 0.044 0.128 0.828
#> GSM152973 4 0.5742 0.615 0.000 0.052 0.300 0.648
#> GSM152974 2 0.0000 0.847 0.000 1.000 0.000 0.000
#> GSM152975 4 0.4985 0.139 0.000 0.468 0.000 0.532
#> GSM152976 4 0.3674 0.839 0.000 0.044 0.104 0.852
#> GSM152977 4 0.2996 0.879 0.000 0.044 0.064 0.892
#> GSM152978 4 0.4370 0.860 0.000 0.044 0.156 0.800
#> GSM152979 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM152980 4 0.7239 0.496 0.000 0.344 0.156 0.500
#> GSM152981 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM152982 4 0.4609 0.858 0.000 0.056 0.156 0.788
#> GSM152983 4 0.2814 0.821 0.000 0.132 0.000 0.868
#> GSM152984 4 0.4948 0.236 0.000 0.440 0.000 0.560
#> GSM152985 4 0.4322 0.862 0.000 0.044 0.152 0.804
#> GSM152986 4 0.1302 0.881 0.000 0.044 0.000 0.956
#> GSM152987 1 0.5255 0.634 0.696 0.004 0.028 0.272
#> GSM152988 4 0.1637 0.876 0.000 0.060 0.000 0.940
#> GSM152989 4 0.2376 0.872 0.012 0.040 0.020 0.928
#> GSM152990 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM152991 3 0.4382 0.902 0.000 0.296 0.704 0.000
#> GSM187524 1 0.0927 0.962 0.976 0.000 0.008 0.016
#> GSM187525 1 0.0927 0.962 0.976 0.000 0.008 0.016
#> GSM187526 1 0.0927 0.962 0.976 0.000 0.008 0.016
#> GSM187527 1 0.2081 0.920 0.916 0.000 0.084 0.000
#> GSM152856 1 0.1256 0.960 0.964 0.000 0.008 0.028
#> GSM152857 1 0.0817 0.958 0.976 0.000 0.024 0.000
#> GSM152858 1 0.0927 0.962 0.976 0.000 0.008 0.016
#> GSM152859 1 0.0927 0.962 0.976 0.000 0.008 0.016
#> GSM152860 1 0.0927 0.962 0.976 0.000 0.008 0.016
#> GSM152861 1 0.0000 0.964 1.000 0.000 0.000 0.000
#> GSM152862 1 0.0927 0.962 0.976 0.000 0.008 0.016
#> GSM152863 1 0.0000 0.964 1.000 0.000 0.000 0.000
#> GSM152864 1 0.1256 0.960 0.964 0.000 0.008 0.028
#> GSM152865 1 0.0000 0.964 1.000 0.000 0.000 0.000
#> GSM152866 1 0.0188 0.964 0.996 0.000 0.004 0.000
#> GSM152867 1 0.1256 0.960 0.964 0.000 0.008 0.028
#> GSM152868 1 0.0804 0.963 0.980 0.000 0.008 0.012
#> GSM152869 1 0.0336 0.964 0.992 0.000 0.008 0.000
#> GSM152870 1 0.0927 0.962 0.976 0.000 0.008 0.016
#> GSM152871 1 0.0336 0.964 0.992 0.000 0.000 0.008
#> GSM152872 1 0.0927 0.962 0.976 0.000 0.008 0.016
#> GSM152873 1 0.1256 0.960 0.964 0.000 0.008 0.028
#> GSM152874 1 0.1256 0.960 0.964 0.000 0.008 0.028
#> GSM152875 1 0.0592 0.963 0.984 0.000 0.000 0.016
#> GSM152876 1 0.0000 0.964 1.000 0.000 0.000 0.000
#> GSM152877 1 0.1256 0.960 0.964 0.000 0.008 0.028
#> GSM152878 1 0.1256 0.960 0.964 0.000 0.008 0.028
#> GSM152879 1 0.1256 0.960 0.964 0.000 0.008 0.028
#> GSM152880 1 0.1256 0.960 0.964 0.000 0.008 0.028
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.3291 0.8277 0.000 0.840 0.000 0.120 0.040
#> GSM152805 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM152806 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM152807 2 0.2304 0.8713 0.000 0.908 0.000 0.044 0.048
#> GSM152808 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM152809 2 0.1862 0.8836 0.000 0.932 0.004 0.016 0.048
#> GSM152810 3 0.3916 0.6062 0.000 0.000 0.732 0.256 0.012
#> GSM152811 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM152812 2 0.1518 0.8851 0.000 0.944 0.004 0.004 0.048
#> GSM152813 2 0.2228 0.8726 0.000 0.912 0.000 0.040 0.048
#> GSM152814 2 0.2228 0.8726 0.000 0.912 0.000 0.040 0.048
#> GSM152815 2 0.2719 0.8614 0.000 0.884 0.000 0.068 0.048
#> GSM152816 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM152817 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM152818 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM152819 3 0.1444 0.9281 0.000 0.040 0.948 0.000 0.012
#> GSM152820 2 0.3151 0.7886 0.000 0.836 0.144 0.000 0.020
#> GSM152821 2 0.0671 0.8853 0.000 0.980 0.004 0.000 0.016
#> GSM153115 4 0.0000 0.8779 0.000 0.000 0.000 1.000 0.000
#> GSM153116 3 0.1628 0.9202 0.000 0.056 0.936 0.000 0.008
#> GSM153117 2 0.2824 0.8170 0.000 0.864 0.116 0.000 0.020
#> GSM153118 2 0.0324 0.8867 0.000 0.992 0.004 0.000 0.004
#> GSM153119 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153120 4 0.0740 0.8743 0.000 0.008 0.008 0.980 0.004
#> GSM153121 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153122 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153123 2 0.0671 0.8876 0.000 0.980 0.004 0.000 0.016
#> GSM153124 2 0.4276 0.4965 0.000 0.616 0.000 0.380 0.004
#> GSM153125 4 0.0162 0.8769 0.000 0.004 0.000 0.996 0.000
#> GSM153126 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153127 2 0.1518 0.8851 0.000 0.944 0.004 0.004 0.048
#> GSM153128 3 0.2338 0.8048 0.000 0.000 0.884 0.112 0.004
#> GSM153129 2 0.0771 0.8847 0.000 0.976 0.004 0.000 0.020
#> GSM153130 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153131 3 0.4042 0.6925 0.000 0.212 0.756 0.032 0.000
#> GSM153132 2 0.3586 0.7451 0.000 0.792 0.188 0.000 0.020
#> GSM153133 2 0.0566 0.8858 0.000 0.984 0.004 0.000 0.012
#> GSM153134 2 0.1059 0.8848 0.000 0.968 0.008 0.004 0.020
#> GSM153135 2 0.1357 0.8847 0.000 0.948 0.000 0.004 0.048
#> GSM153136 4 0.4210 0.1560 0.000 0.412 0.000 0.588 0.000
#> GSM153137 2 0.4504 0.5502 0.000 0.648 0.008 0.336 0.008
#> GSM153138 2 0.2067 0.8768 0.000 0.920 0.000 0.032 0.048
#> GSM153139 3 0.1914 0.9103 0.000 0.060 0.924 0.000 0.016
#> GSM153140 2 0.2378 0.8697 0.000 0.904 0.000 0.048 0.048
#> GSM153141 2 0.1981 0.8788 0.000 0.924 0.000 0.028 0.048
#> GSM153142 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153143 2 0.1357 0.8847 0.000 0.948 0.000 0.004 0.048
#> GSM153144 2 0.0865 0.8871 0.000 0.972 0.004 0.000 0.024
#> GSM153145 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153146 2 0.0671 0.8853 0.000 0.980 0.004 0.000 0.016
#> GSM153147 2 0.0771 0.8847 0.000 0.976 0.004 0.000 0.020
#> GSM153148 2 0.1518 0.8851 0.000 0.944 0.004 0.004 0.048
#> GSM153149 2 0.0771 0.8847 0.000 0.976 0.004 0.000 0.020
#> GSM153150 4 0.4252 0.4003 0.000 0.340 0.008 0.652 0.000
#> GSM153151 2 0.0671 0.8863 0.000 0.980 0.004 0.000 0.016
#> GSM153152 2 0.0771 0.8847 0.000 0.976 0.004 0.000 0.020
#> GSM153153 2 0.0771 0.8847 0.000 0.976 0.004 0.000 0.020
#> GSM153154 2 0.4132 0.6430 0.000 0.720 0.260 0.000 0.020
#> GSM153155 2 0.1357 0.8852 0.000 0.948 0.000 0.004 0.048
#> GSM153156 3 0.2069 0.8953 0.000 0.076 0.912 0.000 0.012
#> GSM153157 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153158 3 0.2351 0.8793 0.000 0.088 0.896 0.000 0.016
#> GSM153159 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153160 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153161 2 0.1518 0.8851 0.000 0.944 0.004 0.004 0.048
#> GSM153162 2 0.0771 0.8847 0.000 0.976 0.004 0.000 0.020
#> GSM153163 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153164 2 0.0771 0.8847 0.000 0.976 0.004 0.000 0.020
#> GSM153165 3 0.0963 0.9373 0.000 0.036 0.964 0.000 0.000
#> GSM153166 2 0.0771 0.8847 0.000 0.976 0.004 0.000 0.020
#> GSM153167 2 0.0771 0.8847 0.000 0.976 0.004 0.000 0.020
#> GSM153168 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153169 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153170 2 0.3476 0.7617 0.000 0.804 0.176 0.000 0.020
#> GSM153171 4 0.0000 0.8779 0.000 0.000 0.000 1.000 0.000
#> GSM153172 2 0.1357 0.8850 0.000 0.948 0.004 0.000 0.048
#> GSM153173 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM153174 2 0.0566 0.8858 0.000 0.984 0.004 0.000 0.012
#> GSM153175 4 0.0000 0.8779 0.000 0.000 0.000 1.000 0.000
#> GSM153176 3 0.4538 0.3937 0.000 0.000 0.620 0.364 0.016
#> GSM153177 2 0.0771 0.8847 0.000 0.976 0.004 0.000 0.020
#> GSM152931 4 0.0000 0.8779 0.000 0.000 0.000 1.000 0.000
#> GSM152932 2 0.1356 0.8880 0.000 0.956 0.004 0.012 0.028
#> GSM152933 2 0.0771 0.8847 0.000 0.976 0.004 0.000 0.020
#> GSM152934 2 0.4567 0.5149 0.000 0.628 0.012 0.356 0.004
#> GSM152935 2 0.0771 0.8847 0.000 0.976 0.004 0.000 0.020
#> GSM152936 2 0.4354 0.5058 0.000 0.624 0.008 0.368 0.000
#> GSM152937 3 0.4347 0.5890 0.000 0.024 0.716 0.256 0.004
#> GSM152938 2 0.3912 0.6880 0.000 0.752 0.228 0.000 0.020
#> GSM152939 4 0.3452 0.6104 0.000 0.244 0.000 0.756 0.000
#> GSM152940 4 0.0740 0.8743 0.000 0.008 0.008 0.980 0.004
#> GSM152941 4 0.5402 0.2218 0.068 0.000 0.004 0.612 0.316
#> GSM152942 3 0.1124 0.9358 0.000 0.036 0.960 0.000 0.004
#> GSM152943 2 0.4353 0.5691 0.000 0.660 0.008 0.328 0.004
#> GSM152944 3 0.1043 0.9344 0.000 0.040 0.960 0.000 0.000
#> GSM152945 2 0.1197 0.8850 0.000 0.952 0.000 0.000 0.048
#> GSM152946 2 0.3355 0.8207 0.000 0.832 0.000 0.132 0.036
#> GSM152947 4 0.0162 0.8772 0.000 0.000 0.000 0.996 0.004
#> GSM152948 2 0.2588 0.8652 0.000 0.892 0.000 0.060 0.048
#> GSM152949 2 0.2824 0.8184 0.000 0.864 0.116 0.000 0.020
#> GSM152950 2 0.1485 0.8756 0.000 0.948 0.032 0.000 0.020
#> GSM152951 2 0.2450 0.8680 0.000 0.900 0.000 0.052 0.048
#> GSM152952 2 0.1484 0.8846 0.000 0.944 0.000 0.008 0.048
#> GSM152953 2 0.1518 0.8851 0.000 0.944 0.004 0.004 0.048
#> GSM152954 4 0.2017 0.8110 0.000 0.080 0.008 0.912 0.000
#> GSM152955 2 0.1408 0.8822 0.000 0.948 0.000 0.044 0.008
#> GSM152956 2 0.1518 0.8851 0.000 0.944 0.004 0.004 0.048
#> GSM152957 4 0.0671 0.8712 0.000 0.000 0.004 0.980 0.016
#> GSM152958 4 0.0613 0.8744 0.000 0.004 0.008 0.984 0.004
#> GSM152959 4 0.0854 0.8721 0.000 0.004 0.008 0.976 0.012
#> GSM152960 2 0.4367 0.4977 0.000 0.620 0.008 0.372 0.000
#> GSM152961 4 0.0000 0.8779 0.000 0.000 0.000 1.000 0.000
#> GSM152962 2 0.0771 0.8847 0.000 0.976 0.004 0.000 0.020
#> GSM152963 2 0.1518 0.8851 0.000 0.944 0.004 0.004 0.048
#> GSM152964 3 0.3916 0.6062 0.000 0.000 0.732 0.256 0.012
#> GSM152965 2 0.0671 0.8863 0.000 0.980 0.004 0.000 0.016
#> GSM152966 4 0.0000 0.8779 0.000 0.000 0.000 1.000 0.000
#> GSM152967 2 0.1800 0.8817 0.000 0.932 0.000 0.020 0.048
#> GSM152968 2 0.3278 0.7793 0.000 0.824 0.156 0.000 0.020
#> GSM152969 4 0.0000 0.8779 0.000 0.000 0.000 1.000 0.000
#> GSM152970 4 0.0771 0.8697 0.000 0.000 0.004 0.976 0.020
#> GSM152971 4 0.0162 0.8769 0.000 0.004 0.000 0.996 0.000
#> GSM152972 4 0.2112 0.8071 0.000 0.084 0.004 0.908 0.004
#> GSM152973 4 0.1195 0.8623 0.000 0.000 0.012 0.960 0.028
#> GSM152974 2 0.0324 0.8871 0.000 0.992 0.004 0.000 0.004
#> GSM152975 2 0.3957 0.6639 0.000 0.712 0.000 0.280 0.008
#> GSM152976 4 0.0703 0.8698 0.000 0.000 0.000 0.976 0.024
#> GSM152977 4 0.0671 0.8712 0.000 0.000 0.004 0.980 0.016
#> GSM152978 4 0.3937 0.6030 0.000 0.252 0.008 0.736 0.004
#> GSM152979 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM152980 2 0.3578 0.7471 0.000 0.784 0.008 0.204 0.004
#> GSM152981 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM152982 2 0.4353 0.5689 0.000 0.660 0.008 0.328 0.004
#> GSM152983 2 0.4456 0.5942 0.000 0.660 0.000 0.320 0.020
#> GSM152984 2 0.4026 0.7049 0.000 0.736 0.000 0.244 0.020
#> GSM152985 4 0.0740 0.8732 0.000 0.004 0.008 0.980 0.008
#> GSM152986 4 0.0000 0.8779 0.000 0.000 0.000 1.000 0.000
#> GSM152987 4 0.5638 -0.0039 0.068 0.000 0.004 0.532 0.396
#> GSM152988 2 0.4430 0.2977 0.000 0.540 0.000 0.456 0.004
#> GSM152989 4 0.0865 0.8664 0.000 0.000 0.004 0.972 0.024
#> GSM152990 3 0.0880 0.9396 0.000 0.032 0.968 0.000 0.000
#> GSM152991 3 0.1251 0.9335 0.000 0.036 0.956 0.000 0.008
#> GSM187524 5 0.2074 0.9473 0.104 0.000 0.000 0.000 0.896
#> GSM187525 5 0.2074 0.9473 0.104 0.000 0.000 0.000 0.896
#> GSM187526 5 0.2074 0.9473 0.104 0.000 0.000 0.000 0.896
#> GSM187527 1 0.3895 0.6808 0.680 0.000 0.000 0.000 0.320
#> GSM152856 1 0.0000 0.8412 1.000 0.000 0.000 0.000 0.000
#> GSM152857 1 0.4252 0.7210 0.700 0.000 0.020 0.000 0.280
#> GSM152858 5 0.2074 0.9473 0.104 0.000 0.000 0.000 0.896
#> GSM152859 5 0.2074 0.9473 0.104 0.000 0.000 0.000 0.896
#> GSM152860 5 0.2074 0.9473 0.104 0.000 0.000 0.000 0.896
#> GSM152861 1 0.3210 0.7913 0.788 0.000 0.000 0.000 0.212
#> GSM152862 5 0.2074 0.9473 0.104 0.000 0.000 0.000 0.896
#> GSM152863 1 0.3586 0.7317 0.736 0.000 0.000 0.000 0.264
#> GSM152864 1 0.0000 0.8412 1.000 0.000 0.000 0.000 0.000
#> GSM152865 1 0.3274 0.7864 0.780 0.000 0.000 0.000 0.220
#> GSM152866 1 0.3336 0.7796 0.772 0.000 0.000 0.000 0.228
#> GSM152867 1 0.0000 0.8412 1.000 0.000 0.000 0.000 0.000
#> GSM152868 1 0.1851 0.8415 0.912 0.000 0.000 0.000 0.088
#> GSM152869 1 0.3336 0.7800 0.772 0.000 0.000 0.000 0.228
#> GSM152870 5 0.2074 0.9473 0.104 0.000 0.000 0.000 0.896
#> GSM152871 5 0.4256 0.1613 0.436 0.000 0.000 0.000 0.564
#> GSM152872 5 0.2074 0.9473 0.104 0.000 0.000 0.000 0.896
#> GSM152873 1 0.0000 0.8412 1.000 0.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.8412 1.000 0.000 0.000 0.000 0.000
#> GSM152875 1 0.1197 0.8453 0.952 0.000 0.000 0.000 0.048
#> GSM152876 1 0.3452 0.7590 0.756 0.000 0.000 0.000 0.244
#> GSM152877 1 0.0290 0.8408 0.992 0.000 0.000 0.000 0.008
#> GSM152878 1 0.1908 0.8406 0.908 0.000 0.000 0.000 0.092
#> GSM152879 1 0.0000 0.8412 1.000 0.000 0.000 0.000 0.000
#> GSM152880 1 0.0290 0.8408 0.992 0.000 0.000 0.000 0.008
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.0632 0.8813 0.000 0.976 0.000 0.024 0.000 0.000
#> GSM152805 5 0.0000 0.8674 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152806 5 0.0000 0.8674 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152807 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152808 5 0.0000 0.8674 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152809 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152810 5 0.4030 0.6787 0.000 0.000 0.140 0.104 0.756 0.000
#> GSM152811 5 0.0000 0.8674 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152812 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152813 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152814 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152815 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152816 5 0.0146 0.8676 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM152817 5 0.0000 0.8674 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152818 5 0.0000 0.8674 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM152819 5 0.3288 0.7323 0.000 0.000 0.276 0.000 0.724 0.000
#> GSM152820 3 0.3370 0.8419 0.000 0.124 0.812 0.000 0.064 0.000
#> GSM152821 3 0.2941 0.9119 0.000 0.220 0.780 0.000 0.000 0.000
#> GSM153115 4 0.1814 0.8482 0.000 0.100 0.000 0.900 0.000 0.000
#> GSM153116 5 0.3782 0.6118 0.000 0.004 0.360 0.000 0.636 0.000
#> GSM153117 3 0.2531 0.8834 0.000 0.132 0.856 0.000 0.012 0.000
#> GSM153118 3 0.3869 0.3451 0.000 0.500 0.500 0.000 0.000 0.000
#> GSM153119 5 0.0000 0.8674 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153120 4 0.2219 0.8383 0.000 0.136 0.000 0.864 0.000 0.000
#> GSM153121 5 0.1910 0.8478 0.000 0.000 0.108 0.000 0.892 0.000
#> GSM153122 5 0.0000 0.8674 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153123 2 0.3175 0.5609 0.000 0.744 0.256 0.000 0.000 0.000
#> GSM153124 2 0.2527 0.7490 0.000 0.832 0.000 0.168 0.000 0.000
#> GSM153125 4 0.2219 0.8375 0.000 0.136 0.000 0.864 0.000 0.000
#> GSM153126 5 0.1327 0.8607 0.000 0.000 0.064 0.000 0.936 0.000
#> GSM153127 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM153128 5 0.2768 0.8103 0.000 0.000 0.156 0.012 0.832 0.000
#> GSM153129 3 0.2854 0.9159 0.000 0.208 0.792 0.000 0.000 0.000
#> GSM153130 5 0.0000 0.8674 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153131 5 0.4930 0.5310 0.000 0.044 0.352 0.016 0.588 0.000
#> GSM153132 3 0.2581 0.8800 0.000 0.128 0.856 0.000 0.016 0.000
#> GSM153133 3 0.2996 0.9051 0.000 0.228 0.772 0.000 0.000 0.000
#> GSM153134 3 0.2996 0.9031 0.000 0.228 0.772 0.000 0.000 0.000
#> GSM153135 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM153136 4 0.3747 0.4824 0.000 0.396 0.000 0.604 0.000 0.000
#> GSM153137 2 0.1556 0.8488 0.000 0.920 0.000 0.080 0.000 0.000
#> GSM153138 2 0.1075 0.8611 0.000 0.952 0.048 0.000 0.000 0.000
#> GSM153139 5 0.3969 0.6368 0.000 0.016 0.332 0.000 0.652 0.000
#> GSM153140 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM153141 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM153142 5 0.0865 0.8661 0.000 0.000 0.036 0.000 0.964 0.000
#> GSM153143 2 0.0632 0.8773 0.000 0.976 0.024 0.000 0.000 0.000
#> GSM153144 2 0.1663 0.8304 0.000 0.912 0.088 0.000 0.000 0.000
#> GSM153145 5 0.0000 0.8674 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153146 3 0.2941 0.9119 0.000 0.220 0.780 0.000 0.000 0.000
#> GSM153147 3 0.2883 0.9156 0.000 0.212 0.788 0.000 0.000 0.000
#> GSM153148 2 0.0547 0.8800 0.000 0.980 0.020 0.000 0.000 0.000
#> GSM153149 3 0.2883 0.9156 0.000 0.212 0.788 0.000 0.000 0.000
#> GSM153150 4 0.3563 0.6295 0.000 0.336 0.000 0.664 0.000 0.000
#> GSM153151 3 0.2969 0.9093 0.000 0.224 0.776 0.000 0.000 0.000
#> GSM153152 3 0.2823 0.9160 0.000 0.204 0.796 0.000 0.000 0.000
#> GSM153153 3 0.2883 0.9146 0.000 0.212 0.788 0.000 0.000 0.000
#> GSM153154 3 0.2706 0.8734 0.000 0.124 0.852 0.000 0.024 0.000
#> GSM153155 2 0.1075 0.8607 0.000 0.952 0.048 0.000 0.000 0.000
#> GSM153156 5 0.3872 0.5522 0.000 0.004 0.392 0.000 0.604 0.000
#> GSM153157 5 0.0000 0.8674 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153158 5 0.4167 0.5671 0.000 0.020 0.368 0.000 0.612 0.000
#> GSM153159 5 0.0260 0.8680 0.000 0.000 0.008 0.000 0.992 0.000
#> GSM153160 5 0.1075 0.8660 0.000 0.000 0.048 0.000 0.952 0.000
#> GSM153161 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM153162 3 0.2805 0.9077 0.000 0.184 0.812 0.000 0.004 0.000
#> GSM153163 5 0.0146 0.8679 0.000 0.000 0.004 0.000 0.996 0.000
#> GSM153164 3 0.2854 0.9159 0.000 0.208 0.792 0.000 0.000 0.000
#> GSM153165 5 0.1387 0.8600 0.000 0.000 0.068 0.000 0.932 0.000
#> GSM153166 3 0.2823 0.9160 0.000 0.204 0.796 0.000 0.000 0.000
#> GSM153167 3 0.2996 0.9065 0.000 0.228 0.772 0.000 0.000 0.000
#> GSM153168 5 0.0000 0.8674 0.000 0.000 0.000 0.000 1.000 0.000
#> GSM153169 5 0.0260 0.8680 0.000 0.000 0.008 0.000 0.992 0.000
#> GSM153170 3 0.2581 0.8800 0.000 0.128 0.856 0.000 0.016 0.000
#> GSM153171 4 0.1714 0.8471 0.000 0.092 0.000 0.908 0.000 0.000
#> GSM153172 2 0.0260 0.8862 0.000 0.992 0.008 0.000 0.000 0.000
#> GSM153173 5 0.0790 0.8665 0.000 0.000 0.032 0.000 0.968 0.000
#> GSM153174 3 0.3810 0.5661 0.000 0.428 0.572 0.000 0.000 0.000
#> GSM153175 4 0.1765 0.8478 0.000 0.096 0.000 0.904 0.000 0.000
#> GSM153176 4 0.4157 0.2761 0.000 0.000 0.012 0.544 0.444 0.000
#> GSM153177 3 0.2823 0.9160 0.000 0.204 0.796 0.000 0.000 0.000
#> GSM152931 4 0.1765 0.8480 0.000 0.096 0.000 0.904 0.000 0.000
#> GSM152932 2 0.2491 0.7007 0.000 0.836 0.164 0.000 0.000 0.000
#> GSM152933 3 0.2912 0.9135 0.000 0.216 0.784 0.000 0.000 0.000
#> GSM152934 2 0.5891 0.2902 0.000 0.468 0.232 0.300 0.000 0.000
#> GSM152935 3 0.2883 0.9156 0.000 0.212 0.788 0.000 0.000 0.000
#> GSM152936 2 0.2762 0.7095 0.000 0.804 0.000 0.196 0.000 0.000
#> GSM152937 5 0.4894 0.6182 0.000 0.000 0.376 0.068 0.556 0.000
#> GSM152938 3 0.4771 0.5452 0.000 0.100 0.652 0.000 0.248 0.000
#> GSM152939 4 0.3706 0.5215 0.000 0.380 0.000 0.620 0.000 0.000
#> GSM152940 4 0.2527 0.8197 0.000 0.168 0.000 0.832 0.000 0.000
#> GSM152941 6 0.4715 0.3881 0.004 0.000 0.036 0.452 0.000 0.508
#> GSM152942 5 0.3409 0.7002 0.000 0.000 0.300 0.000 0.700 0.000
#> GSM152943 2 0.3229 0.7931 0.000 0.816 0.044 0.140 0.000 0.000
#> GSM152944 5 0.2994 0.7887 0.000 0.004 0.208 0.000 0.788 0.000
#> GSM152945 2 0.1075 0.8610 0.000 0.952 0.048 0.000 0.000 0.000
#> GSM152946 2 0.0632 0.8817 0.000 0.976 0.000 0.024 0.000 0.000
#> GSM152947 4 0.1007 0.8284 0.000 0.044 0.000 0.956 0.000 0.000
#> GSM152948 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152949 3 0.2473 0.8865 0.000 0.136 0.856 0.000 0.008 0.000
#> GSM152950 3 0.2442 0.8901 0.000 0.144 0.852 0.000 0.004 0.000
#> GSM152951 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152952 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152953 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152954 4 0.3351 0.7051 0.000 0.288 0.000 0.712 0.000 0.000
#> GSM152955 2 0.4154 0.2748 0.000 0.652 0.324 0.020 0.004 0.000
#> GSM152956 2 0.0000 0.8893 0.000 1.000 0.000 0.000 0.000 0.000
#> GSM152957 4 0.0405 0.8038 0.000 0.004 0.008 0.988 0.000 0.000
#> GSM152958 4 0.2048 0.8439 0.000 0.120 0.000 0.880 0.000 0.000
#> GSM152959 4 0.0405 0.8038 0.000 0.004 0.008 0.988 0.000 0.000
#> GSM152960 2 0.3843 -0.0150 0.000 0.548 0.000 0.452 0.000 0.000
#> GSM152961 4 0.0405 0.8080 0.000 0.008 0.004 0.988 0.000 0.000
#> GSM152962 3 0.2491 0.8993 0.000 0.164 0.836 0.000 0.000 0.000
#> GSM152963 2 0.0363 0.8844 0.000 0.988 0.012 0.000 0.000 0.000
#> GSM152964 5 0.4085 0.6738 0.000 0.000 0.128 0.120 0.752 0.000
#> GSM152965 3 0.2969 0.9093 0.000 0.224 0.776 0.000 0.000 0.000
#> GSM152966 4 0.1765 0.8480 0.000 0.096 0.000 0.904 0.000 0.000
#> GSM152967 2 0.0632 0.8773 0.000 0.976 0.024 0.000 0.000 0.000
#> GSM152968 3 0.2667 0.8780 0.000 0.128 0.852 0.000 0.020 0.000
#> GSM152969 4 0.1814 0.8480 0.000 0.100 0.000 0.900 0.000 0.000
#> GSM152970 4 0.0405 0.8038 0.000 0.004 0.008 0.988 0.000 0.000
#> GSM152971 4 0.2378 0.8304 0.000 0.152 0.000 0.848 0.000 0.000
#> GSM152972 4 0.3351 0.7047 0.000 0.288 0.000 0.712 0.000 0.000
#> GSM152973 4 0.3105 0.7869 0.000 0.064 0.008 0.848 0.080 0.000
#> GSM152974 2 0.2631 0.7017 0.000 0.820 0.180 0.000 0.000 0.000
#> GSM152975 2 0.1327 0.8597 0.000 0.936 0.000 0.064 0.000 0.000
#> GSM152976 4 0.0405 0.8038 0.000 0.004 0.008 0.988 0.000 0.000
#> GSM152977 4 0.0622 0.8101 0.000 0.012 0.008 0.980 0.000 0.000
#> GSM152978 4 0.3563 0.6279 0.000 0.336 0.000 0.664 0.000 0.000
#> GSM152979 5 0.2416 0.8244 0.000 0.000 0.156 0.000 0.844 0.000
#> GSM152980 2 0.1492 0.8738 0.000 0.940 0.036 0.024 0.000 0.000
#> GSM152981 5 0.1387 0.8602 0.000 0.000 0.068 0.000 0.932 0.000
#> GSM152982 2 0.4014 0.7376 0.000 0.756 0.096 0.148 0.000 0.000
#> GSM152983 2 0.1501 0.8516 0.000 0.924 0.000 0.076 0.000 0.000
#> GSM152984 2 0.1745 0.8560 0.000 0.920 0.012 0.068 0.000 0.000
#> GSM152985 4 0.0520 0.8066 0.000 0.008 0.008 0.984 0.000 0.000
#> GSM152986 4 0.1765 0.8480 0.000 0.096 0.000 0.904 0.000 0.000
#> GSM152987 6 0.4682 0.4498 0.004 0.000 0.036 0.420 0.000 0.540
#> GSM152988 2 0.3737 0.2361 0.000 0.608 0.000 0.392 0.000 0.000
#> GSM152989 4 0.1010 0.7839 0.000 0.004 0.036 0.960 0.000 0.000
#> GSM152990 5 0.1814 0.8512 0.000 0.000 0.100 0.000 0.900 0.000
#> GSM152991 5 0.2697 0.8036 0.000 0.000 0.188 0.000 0.812 0.000
#> GSM187524 6 0.0000 0.7788 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM187525 6 0.0000 0.7788 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM187526 6 0.0146 0.7786 0.004 0.000 0.000 0.000 0.000 0.996
#> GSM187527 6 0.4399 0.1330 0.460 0.000 0.024 0.000 0.000 0.516
#> GSM152856 1 0.0000 0.9065 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152857 6 0.4262 0.0902 0.476 0.000 0.016 0.000 0.000 0.508
#> GSM152858 6 0.0146 0.7786 0.004 0.000 0.000 0.000 0.000 0.996
#> GSM152859 6 0.0603 0.7734 0.004 0.000 0.016 0.000 0.000 0.980
#> GSM152860 6 0.0000 0.7788 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152861 1 0.2454 0.8327 0.840 0.000 0.000 0.000 0.000 0.160
#> GSM152862 6 0.0000 0.7788 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152863 6 0.4181 0.0924 0.476 0.000 0.012 0.000 0.000 0.512
#> GSM152864 1 0.0000 0.9065 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152865 1 0.2664 0.8089 0.816 0.000 0.000 0.000 0.000 0.184
#> GSM152866 1 0.2854 0.7808 0.792 0.000 0.000 0.000 0.000 0.208
#> GSM152867 1 0.0000 0.9065 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152868 1 0.0790 0.9021 0.968 0.000 0.000 0.000 0.000 0.032
#> GSM152869 1 0.2597 0.8130 0.824 0.000 0.000 0.000 0.000 0.176
#> GSM152870 6 0.0146 0.7786 0.004 0.000 0.000 0.000 0.000 0.996
#> GSM152871 6 0.3198 0.5510 0.260 0.000 0.000 0.000 0.000 0.740
#> GSM152872 6 0.0000 0.7788 0.000 0.000 0.000 0.000 0.000 1.000
#> GSM152873 1 0.0000 0.9065 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152874 1 0.0000 0.9065 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152875 1 0.1863 0.8689 0.896 0.000 0.000 0.000 0.000 0.104
#> GSM152876 1 0.3404 0.7246 0.760 0.000 0.016 0.000 0.000 0.224
#> GSM152877 1 0.0000 0.9065 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152878 1 0.0865 0.9011 0.964 0.000 0.000 0.000 0.000 0.036
#> GSM152879 1 0.0000 0.9065 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152880 1 0.0000 0.9065 1.000 0.000 0.000 0.000 0.000 0.000
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
#> Error in mat[ceiling(1:nr/h_ratio), ceiling(1:nc/w_ratio), drop = FALSE]: subscript out of bounds
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> ATC:mclust 170 6.66e-31 2
#> ATC:mclust 165 1.75e-33 3
#> ATC:mclust 157 1.95e-29 4
#> ATC:mclust 162 7.70e-30 5
#> ATC:mclust 159 6.28e-30 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
The object with results only for a single top-value method and a single partition method can be extracted as:
res = res_list["ATC", "NMF"]
# you can also extract it by
# res = res_list["ATC:NMF"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6.
#> On a matrix with 11993 rows and 171 columns.
#> Top rows (1000, 2000, 3000, 4000, 5000) are extracted by 'ATC' method.
#> Subgroups are detected by 'NMF' method.
#> Performed in total 1250 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_signatures"
#> [7] "consensus_heatmap" "dimension_reduction" "functional_enrichment"
#> [10] "get_anno_col" "get_anno" "get_classes"
#> [13] "get_consensus" "get_matrix" "get_membership"
#> [16] "get_param" "get_signatures" "get_stats"
#> [19] "is_best_k" "is_stable_k" "membership_heatmap"
#> [22] "ncol" "nrow" "plot_ecdf"
#> [25] "rownames" "select_partition_number" "show"
#> [28] "suggest_best_k" "test_to_known_factors"
collect_plots() function collects all the plots made from res for all k (number of partitions)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, lower PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.893 0.932 0.971 0.4251 0.574 0.574
#> 3 3 0.747 0.855 0.929 0.4959 0.677 0.485
#> 4 4 0.787 0.827 0.920 0.0730 0.829 0.595
#> 5 5 0.564 0.659 0.794 0.0654 0.953 0.858
#> 6 6 0.561 0.603 0.761 0.0643 0.838 0.528
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following shows the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall class
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> GSM152804 2 0.0000 0.9765 0.000 1.000
#> GSM152805 2 0.0000 0.9765 0.000 1.000
#> GSM152806 2 0.0000 0.9765 0.000 1.000
#> GSM152807 2 0.0000 0.9765 0.000 1.000
#> GSM152808 2 0.0000 0.9765 0.000 1.000
#> GSM152809 2 0.0000 0.9765 0.000 1.000
#> GSM152810 2 0.5519 0.8407 0.128 0.872
#> GSM152811 2 0.0000 0.9765 0.000 1.000
#> GSM152812 2 0.0000 0.9765 0.000 1.000
#> GSM152813 2 0.0000 0.9765 0.000 1.000
#> GSM152814 2 0.0000 0.9765 0.000 1.000
#> GSM152815 2 0.0000 0.9765 0.000 1.000
#> GSM152816 2 0.0000 0.9765 0.000 1.000
#> GSM152817 2 0.0000 0.9765 0.000 1.000
#> GSM152818 2 0.0000 0.9765 0.000 1.000
#> GSM152819 2 0.0000 0.9765 0.000 1.000
#> GSM152820 2 0.0000 0.9765 0.000 1.000
#> GSM152821 2 0.0000 0.9765 0.000 1.000
#> GSM153115 2 0.7299 0.7347 0.204 0.796
#> GSM153116 2 0.0000 0.9765 0.000 1.000
#> GSM153117 2 0.0000 0.9765 0.000 1.000
#> GSM153118 2 0.0000 0.9765 0.000 1.000
#> GSM153119 2 0.0000 0.9765 0.000 1.000
#> GSM153120 1 0.0376 0.9498 0.996 0.004
#> GSM153121 2 0.0000 0.9765 0.000 1.000
#> GSM153122 2 0.0000 0.9765 0.000 1.000
#> GSM153123 2 0.0000 0.9765 0.000 1.000
#> GSM153124 2 0.0000 0.9765 0.000 1.000
#> GSM153125 2 0.6973 0.7587 0.188 0.812
#> GSM153126 2 0.0000 0.9765 0.000 1.000
#> GSM153127 2 0.0000 0.9765 0.000 1.000
#> GSM153128 2 0.0000 0.9765 0.000 1.000
#> GSM153129 2 0.0000 0.9765 0.000 1.000
#> GSM153130 2 0.0000 0.9765 0.000 1.000
#> GSM153131 2 0.0000 0.9765 0.000 1.000
#> GSM153132 2 0.0000 0.9765 0.000 1.000
#> GSM153133 2 0.0000 0.9765 0.000 1.000
#> GSM153134 2 0.0000 0.9765 0.000 1.000
#> GSM153135 2 0.0000 0.9765 0.000 1.000
#> GSM153136 2 0.0938 0.9656 0.012 0.988
#> GSM153137 2 0.7528 0.7160 0.216 0.784
#> GSM153138 2 0.0000 0.9765 0.000 1.000
#> GSM153139 2 0.0000 0.9765 0.000 1.000
#> GSM153140 2 0.0000 0.9765 0.000 1.000
#> GSM153141 2 0.0000 0.9765 0.000 1.000
#> GSM153142 2 0.0000 0.9765 0.000 1.000
#> GSM153143 2 0.0000 0.9765 0.000 1.000
#> GSM153144 2 0.0000 0.9765 0.000 1.000
#> GSM153145 2 0.0000 0.9765 0.000 1.000
#> GSM153146 2 0.0000 0.9765 0.000 1.000
#> GSM153147 2 0.0000 0.9765 0.000 1.000
#> GSM153148 2 0.0000 0.9765 0.000 1.000
#> GSM153149 2 0.0000 0.9765 0.000 1.000
#> GSM153150 1 0.8207 0.6789 0.744 0.256
#> GSM153151 2 0.0000 0.9765 0.000 1.000
#> GSM153152 2 0.0000 0.9765 0.000 1.000
#> GSM153153 2 0.0000 0.9765 0.000 1.000
#> GSM153154 2 0.0000 0.9765 0.000 1.000
#> GSM153155 2 0.0000 0.9765 0.000 1.000
#> GSM153156 2 0.0000 0.9765 0.000 1.000
#> GSM153157 2 0.0000 0.9765 0.000 1.000
#> GSM153158 2 0.0000 0.9765 0.000 1.000
#> GSM153159 2 0.0000 0.9765 0.000 1.000
#> GSM153160 2 0.0000 0.9765 0.000 1.000
#> GSM153161 2 0.0000 0.9765 0.000 1.000
#> GSM153162 2 0.0000 0.9765 0.000 1.000
#> GSM153163 2 0.0000 0.9765 0.000 1.000
#> GSM153164 2 0.0000 0.9765 0.000 1.000
#> GSM153165 2 0.0000 0.9765 0.000 1.000
#> GSM153166 2 0.0000 0.9765 0.000 1.000
#> GSM153167 2 0.0000 0.9765 0.000 1.000
#> GSM153168 2 0.0000 0.9765 0.000 1.000
#> GSM153169 2 0.0000 0.9765 0.000 1.000
#> GSM153170 2 0.0000 0.9765 0.000 1.000
#> GSM153171 1 0.9044 0.5612 0.680 0.320
#> GSM153172 2 0.0000 0.9765 0.000 1.000
#> GSM153173 2 0.0000 0.9765 0.000 1.000
#> GSM153174 2 0.0000 0.9765 0.000 1.000
#> GSM153175 2 0.9087 0.5080 0.324 0.676
#> GSM153176 2 0.0000 0.9765 0.000 1.000
#> GSM153177 2 0.0000 0.9765 0.000 1.000
#> GSM152931 2 0.8499 0.6093 0.276 0.724
#> GSM152932 2 0.0000 0.9765 0.000 1.000
#> GSM152933 2 0.0000 0.9765 0.000 1.000
#> GSM152934 2 0.8267 0.6404 0.260 0.740
#> GSM152935 2 0.0000 0.9765 0.000 1.000
#> GSM152936 2 0.9491 0.3993 0.368 0.632
#> GSM152937 2 0.0000 0.9765 0.000 1.000
#> GSM152938 2 0.0000 0.9765 0.000 1.000
#> GSM152939 2 0.0000 0.9765 0.000 1.000
#> GSM152940 1 0.0000 0.9522 1.000 0.000
#> GSM152941 1 0.0000 0.9522 1.000 0.000
#> GSM152942 2 0.0000 0.9765 0.000 1.000
#> GSM152943 2 0.2948 0.9264 0.052 0.948
#> GSM152944 2 0.0000 0.9765 0.000 1.000
#> GSM152945 2 0.0000 0.9765 0.000 1.000
#> GSM152946 2 0.0000 0.9765 0.000 1.000
#> GSM152947 1 0.1414 0.9395 0.980 0.020
#> GSM152948 2 0.0000 0.9765 0.000 1.000
#> GSM152949 2 0.0000 0.9765 0.000 1.000
#> GSM152950 2 0.0000 0.9765 0.000 1.000
#> GSM152951 2 0.0000 0.9765 0.000 1.000
#> GSM152952 2 0.0000 0.9765 0.000 1.000
#> GSM152953 2 0.0000 0.9765 0.000 1.000
#> GSM152954 1 0.2778 0.9183 0.952 0.048
#> GSM152955 2 0.0000 0.9765 0.000 1.000
#> GSM152956 2 0.0000 0.9765 0.000 1.000
#> GSM152957 1 0.1633 0.9366 0.976 0.024
#> GSM152958 1 0.0000 0.9522 1.000 0.000
#> GSM152959 1 0.0000 0.9522 1.000 0.000
#> GSM152960 1 0.8144 0.6855 0.748 0.252
#> GSM152961 1 0.0000 0.9522 1.000 0.000
#> GSM152962 2 0.0000 0.9765 0.000 1.000
#> GSM152963 2 0.0000 0.9765 0.000 1.000
#> GSM152964 2 0.3584 0.9097 0.068 0.932
#> GSM152965 2 0.0000 0.9765 0.000 1.000
#> GSM152966 1 0.9358 0.4912 0.648 0.352
#> GSM152967 2 0.0000 0.9765 0.000 1.000
#> GSM152968 2 0.0000 0.9765 0.000 1.000
#> GSM152969 1 0.5294 0.8542 0.880 0.120
#> GSM152970 1 0.0000 0.9522 1.000 0.000
#> GSM152971 2 0.9998 -0.0221 0.492 0.508
#> GSM152972 1 0.6623 0.7973 0.828 0.172
#> GSM152973 2 0.0000 0.9765 0.000 1.000
#> GSM152974 2 0.0000 0.9765 0.000 1.000
#> GSM152975 2 0.0000 0.9765 0.000 1.000
#> GSM152976 1 0.9866 0.2754 0.568 0.432
#> GSM152977 1 0.5842 0.8338 0.860 0.140
#> GSM152978 1 0.0000 0.9522 1.000 0.000
#> GSM152979 2 0.0000 0.9765 0.000 1.000
#> GSM152980 2 0.0000 0.9765 0.000 1.000
#> GSM152981 2 0.0000 0.9765 0.000 1.000
#> GSM152982 2 0.0000 0.9765 0.000 1.000
#> GSM152983 2 0.0000 0.9765 0.000 1.000
#> GSM152984 2 0.0000 0.9765 0.000 1.000
#> GSM152985 1 0.0000 0.9522 1.000 0.000
#> GSM152986 1 0.6887 0.7825 0.816 0.184
#> GSM152987 1 0.0000 0.9522 1.000 0.000
#> GSM152988 2 0.0000 0.9765 0.000 1.000
#> GSM152989 1 0.0000 0.9522 1.000 0.000
#> GSM152990 2 0.0000 0.9765 0.000 1.000
#> GSM152991 2 0.0000 0.9765 0.000 1.000
#> GSM187524 1 0.0000 0.9522 1.000 0.000
#> GSM187525 1 0.0000 0.9522 1.000 0.000
#> GSM187526 1 0.0000 0.9522 1.000 0.000
#> GSM187527 1 0.0000 0.9522 1.000 0.000
#> GSM152856 1 0.0000 0.9522 1.000 0.000
#> GSM152857 1 0.0000 0.9522 1.000 0.000
#> GSM152858 1 0.0000 0.9522 1.000 0.000
#> GSM152859 1 0.0000 0.9522 1.000 0.000
#> GSM152860 1 0.0000 0.9522 1.000 0.000
#> GSM152861 1 0.0000 0.9522 1.000 0.000
#> GSM152862 1 0.0000 0.9522 1.000 0.000
#> GSM152863 1 0.0000 0.9522 1.000 0.000
#> GSM152864 1 0.0000 0.9522 1.000 0.000
#> GSM152865 1 0.0000 0.9522 1.000 0.000
#> GSM152866 1 0.0000 0.9522 1.000 0.000
#> GSM152867 1 0.0000 0.9522 1.000 0.000
#> GSM152868 1 0.0000 0.9522 1.000 0.000
#> GSM152869 1 0.0000 0.9522 1.000 0.000
#> GSM152870 1 0.0000 0.9522 1.000 0.000
#> GSM152871 1 0.0000 0.9522 1.000 0.000
#> GSM152872 1 0.0000 0.9522 1.000 0.000
#> GSM152873 1 0.0000 0.9522 1.000 0.000
#> GSM152874 1 0.0000 0.9522 1.000 0.000
#> GSM152875 1 0.0000 0.9522 1.000 0.000
#> GSM152876 1 0.0000 0.9522 1.000 0.000
#> GSM152877 1 0.0000 0.9522 1.000 0.000
#> GSM152878 1 0.0000 0.9522 1.000 0.000
#> GSM152879 1 0.0000 0.9522 1.000 0.000
#> GSM152880 1 0.0000 0.9522 1.000 0.000
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> GSM152804 2 0.3686 0.823 0.000 0.860 0.140
#> GSM152805 3 0.0000 0.926 0.000 0.000 1.000
#> GSM152806 3 0.0237 0.925 0.004 0.000 0.996
#> GSM152807 2 0.1031 0.891 0.000 0.976 0.024
#> GSM152808 3 0.0424 0.924 0.008 0.000 0.992
#> GSM152809 2 0.0892 0.892 0.000 0.980 0.020
#> GSM152810 3 0.5058 0.664 0.244 0.000 0.756
#> GSM152811 3 0.0747 0.919 0.016 0.000 0.984
#> GSM152812 2 0.1031 0.891 0.000 0.976 0.024
#> GSM152813 2 0.1411 0.887 0.000 0.964 0.036
#> GSM152814 2 0.2165 0.873 0.000 0.936 0.064
#> GSM152815 2 0.0424 0.891 0.000 0.992 0.008
#> GSM152816 3 0.0000 0.926 0.000 0.000 1.000
#> GSM152817 3 0.0592 0.922 0.012 0.000 0.988
#> GSM152818 3 0.0237 0.925 0.004 0.000 0.996
#> GSM152819 3 0.0000 0.926 0.000 0.000 1.000
#> GSM152820 3 0.0000 0.926 0.000 0.000 1.000
#> GSM152821 3 0.2356 0.888 0.000 0.072 0.928
#> GSM153115 2 0.0000 0.890 0.000 1.000 0.000
#> GSM153116 3 0.0000 0.926 0.000 0.000 1.000
#> GSM153117 3 0.1289 0.914 0.000 0.032 0.968
#> GSM153118 3 0.6008 0.408 0.000 0.372 0.628
#> GSM153119 3 0.0592 0.922 0.012 0.000 0.988
#> GSM153120 2 0.0424 0.885 0.008 0.992 0.000
#> GSM153121 3 0.0000 0.926 0.000 0.000 1.000
#> GSM153122 3 0.0592 0.922 0.012 0.000 0.988
#> GSM153123 2 0.5138 0.690 0.000 0.748 0.252
#> GSM153124 2 0.1860 0.880 0.000 0.948 0.052
#> GSM153125 2 0.0000 0.890 0.000 1.000 0.000
#> GSM153126 3 0.0000 0.926 0.000 0.000 1.000
#> GSM153127 2 0.1031 0.891 0.000 0.976 0.024
#> GSM153128 3 0.1163 0.912 0.028 0.000 0.972
#> GSM153129 3 0.2625 0.879 0.000 0.084 0.916
#> GSM153130 3 0.0000 0.926 0.000 0.000 1.000
#> GSM153131 3 0.0237 0.926 0.000 0.004 0.996
#> GSM153132 3 0.0237 0.926 0.000 0.004 0.996
#> GSM153133 3 0.3412 0.843 0.000 0.124 0.876
#> GSM153134 3 0.5785 0.510 0.000 0.332 0.668
#> GSM153135 2 0.1031 0.891 0.000 0.976 0.024
#> GSM153136 2 0.0000 0.890 0.000 1.000 0.000
#> GSM153137 2 0.0000 0.890 0.000 1.000 0.000
#> GSM153138 2 0.6215 0.302 0.000 0.572 0.428
#> GSM153139 3 0.0000 0.926 0.000 0.000 1.000
#> GSM153140 2 0.1031 0.891 0.000 0.976 0.024
#> GSM153141 2 0.0424 0.891 0.000 0.992 0.008
#> GSM153142 3 0.0237 0.925 0.004 0.000 0.996
#> GSM153143 2 0.2711 0.861 0.000 0.912 0.088
#> GSM153144 2 0.5706 0.579 0.000 0.680 0.320
#> GSM153145 3 0.0237 0.925 0.004 0.000 0.996
#> GSM153146 3 0.2537 0.882 0.000 0.080 0.920
#> GSM153147 3 0.0747 0.921 0.000 0.016 0.984
#> GSM153148 2 0.2959 0.853 0.000 0.900 0.100
#> GSM153149 3 0.1163 0.916 0.000 0.028 0.972
#> GSM153150 2 0.0000 0.890 0.000 1.000 0.000
#> GSM153151 3 0.0424 0.925 0.000 0.008 0.992
#> GSM153152 3 0.1643 0.907 0.000 0.044 0.956
#> GSM153153 3 0.4452 0.766 0.000 0.192 0.808
#> GSM153154 3 0.0000 0.926 0.000 0.000 1.000
#> GSM153155 2 0.6045 0.442 0.000 0.620 0.380
#> GSM153156 3 0.0000 0.926 0.000 0.000 1.000
#> GSM153157 3 0.0592 0.922 0.012 0.000 0.988
#> GSM153158 3 0.0000 0.926 0.000 0.000 1.000
#> GSM153159 3 0.0237 0.925 0.004 0.000 0.996
#> GSM153160 3 0.0000 0.926 0.000 0.000 1.000
#> GSM153161 2 0.0592 0.892 0.000 0.988 0.012
#> GSM153162 3 0.4452 0.766 0.000 0.192 0.808
#> GSM153163 3 0.0000 0.926 0.000 0.000 1.000
#> GSM153164 3 0.3482 0.839 0.000 0.128 0.872
#> GSM153165 3 0.0237 0.926 0.000 0.004 0.996
#> GSM153166 3 0.4346 0.777 0.000 0.184 0.816
#> GSM153167 3 0.4002 0.805 0.000 0.160 0.840
#> GSM153168 3 0.0592 0.922 0.012 0.000 0.988
#> GSM153169 3 0.0237 0.925 0.004 0.000 0.996
#> GSM153170 3 0.0592 0.923 0.000 0.012 0.988
#> GSM153171 2 0.0000 0.890 0.000 1.000 0.000
#> GSM153172 2 0.3340 0.838 0.000 0.880 0.120
#> GSM153173 3 0.0000 0.926 0.000 0.000 1.000
#> GSM153174 3 0.5948 0.441 0.000 0.360 0.640
#> GSM153175 2 0.0000 0.890 0.000 1.000 0.000
#> GSM153176 3 0.0237 0.925 0.004 0.000 0.996
#> GSM153177 3 0.4654 0.743 0.000 0.208 0.792
#> GSM152931 2 0.0000 0.890 0.000 1.000 0.000
#> GSM152932 3 0.6252 0.174 0.000 0.444 0.556
#> GSM152933 3 0.4399 0.771 0.000 0.188 0.812
#> GSM152934 3 0.3340 0.837 0.120 0.000 0.880
#> GSM152935 3 0.3340 0.847 0.000 0.120 0.880
#> GSM152936 2 0.0000 0.890 0.000 1.000 0.000
#> GSM152937 3 0.1411 0.906 0.036 0.000 0.964
#> GSM152938 3 0.0237 0.926 0.000 0.004 0.996
#> GSM152939 2 0.0237 0.891 0.000 0.996 0.004
#> GSM152940 2 0.0424 0.885 0.008 0.992 0.000
#> GSM152941 1 0.3816 0.871 0.852 0.148 0.000
#> GSM152942 3 0.0000 0.926 0.000 0.000 1.000
#> GSM152943 3 0.5810 0.501 0.000 0.336 0.664
#> GSM152944 3 0.0000 0.926 0.000 0.000 1.000
#> GSM152945 2 0.5760 0.564 0.000 0.672 0.328
#> GSM152946 2 0.1529 0.886 0.000 0.960 0.040
#> GSM152947 2 0.0237 0.888 0.004 0.996 0.000
#> GSM152948 2 0.0424 0.891 0.000 0.992 0.008
#> GSM152949 3 0.0237 0.926 0.000 0.004 0.996
#> GSM152950 3 0.0000 0.926 0.000 0.000 1.000
#> GSM152951 2 0.1031 0.891 0.000 0.976 0.024
#> GSM152952 2 0.0000 0.890 0.000 1.000 0.000
#> GSM152953 2 0.1031 0.891 0.000 0.976 0.024
#> GSM152954 2 0.0424 0.885 0.008 0.992 0.000
#> GSM152955 3 0.1411 0.912 0.000 0.036 0.964
#> GSM152956 2 0.0747 0.892 0.000 0.984 0.016
#> GSM152957 2 0.7346 0.131 0.432 0.536 0.032
#> GSM152958 2 0.0237 0.888 0.004 0.996 0.000
#> GSM152959 1 0.1411 0.954 0.964 0.036 0.000
#> GSM152960 2 0.6583 0.722 0.136 0.756 0.108
#> GSM152961 2 0.0424 0.885 0.008 0.992 0.000
#> GSM152962 3 0.0000 0.926 0.000 0.000 1.000
#> GSM152963 2 0.1289 0.889 0.000 0.968 0.032
#> GSM152964 3 0.4750 0.708 0.216 0.000 0.784
#> GSM152965 3 0.2066 0.896 0.000 0.060 0.940
#> GSM152966 2 0.0000 0.890 0.000 1.000 0.000
#> GSM152967 2 0.5760 0.564 0.000 0.672 0.328
#> GSM152968 3 0.0000 0.926 0.000 0.000 1.000
#> GSM152969 2 0.0000 0.890 0.000 1.000 0.000
#> GSM152970 2 0.5465 0.527 0.288 0.712 0.000
#> GSM152971 2 0.0000 0.890 0.000 1.000 0.000
#> GSM152972 2 0.0000 0.890 0.000 1.000 0.000
#> GSM152973 2 0.5529 0.621 0.000 0.704 0.296
#> GSM152974 2 0.5810 0.546 0.000 0.664 0.336
#> GSM152975 2 0.4235 0.786 0.000 0.824 0.176
#> GSM152976 2 0.3192 0.838 0.000 0.888 0.112
#> GSM152977 1 0.6487 0.583 0.700 0.032 0.268
#> GSM152978 2 0.0424 0.885 0.008 0.992 0.000
#> GSM152979 3 0.0237 0.926 0.000 0.004 0.996
#> GSM152980 2 0.5327 0.662 0.000 0.728 0.272
#> GSM152981 3 0.0592 0.922 0.012 0.000 0.988
#> GSM152982 3 0.4346 0.778 0.000 0.184 0.816
#> GSM152983 2 0.0424 0.892 0.000 0.992 0.008
#> GSM152984 2 0.6154 0.359 0.000 0.592 0.408
#> GSM152985 1 0.4842 0.777 0.776 0.224 0.000
#> GSM152986 2 0.0000 0.890 0.000 1.000 0.000
#> GSM152987 1 0.1753 0.950 0.952 0.048 0.000
#> GSM152988 2 0.1163 0.890 0.000 0.972 0.028
#> GSM152989 1 0.0892 0.955 0.980 0.020 0.000
#> GSM152990 3 0.0000 0.926 0.000 0.000 1.000
#> GSM152991 3 0.0237 0.925 0.004 0.000 0.996
#> GSM187524 1 0.0000 0.952 1.000 0.000 0.000
#> GSM187525 1 0.0424 0.954 0.992 0.008 0.000
#> GSM187526 1 0.0592 0.955 0.988 0.012 0.000
#> GSM187527 1 0.2537 0.933 0.920 0.080 0.000
#> GSM152856 1 0.3192 0.908 0.888 0.112 0.000
#> GSM152857 1 0.1031 0.938 0.976 0.000 0.024
#> GSM152858 1 0.0000 0.952 1.000 0.000 0.000
#> GSM152859 1 0.0237 0.950 0.996 0.000 0.004
#> GSM152860 1 0.0000 0.952 1.000 0.000 0.000
#> GSM152861 1 0.0892 0.955 0.980 0.020 0.000
#> GSM152862 1 0.0000 0.952 1.000 0.000 0.000
#> GSM152863 1 0.0000 0.952 1.000 0.000 0.000
#> GSM152864 1 0.1163 0.955 0.972 0.028 0.000
#> GSM152865 1 0.0592 0.955 0.988 0.012 0.000
#> GSM152866 1 0.0592 0.955 0.988 0.012 0.000
#> GSM152867 1 0.1860 0.949 0.948 0.052 0.000
#> GSM152868 1 0.2625 0.930 0.916 0.084 0.000
#> GSM152869 1 0.1860 0.949 0.948 0.052 0.000
#> GSM152870 1 0.0000 0.952 1.000 0.000 0.000
#> GSM152871 1 0.0592 0.955 0.988 0.012 0.000
#> GSM152872 1 0.0000 0.952 1.000 0.000 0.000
#> GSM152873 1 0.1289 0.954 0.968 0.032 0.000
#> GSM152874 1 0.1411 0.954 0.964 0.036 0.000
#> GSM152875 1 0.0592 0.955 0.988 0.012 0.000
#> GSM152876 1 0.2959 0.918 0.900 0.100 0.000
#> GSM152877 1 0.1753 0.950 0.952 0.048 0.000
#> GSM152878 1 0.3686 0.880 0.860 0.140 0.000
#> GSM152879 1 0.2537 0.933 0.920 0.080 0.000
#> GSM152880 1 0.1163 0.955 0.972 0.028 0.000
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> GSM152804 2 0.4459 0.7615 0.032 0.780 0.188 0.000
#> GSM152805 3 0.0336 0.9451 0.000 0.000 0.992 0.008
#> GSM152806 3 0.0188 0.9462 0.000 0.000 0.996 0.004
#> GSM152807 2 0.0469 0.9107 0.012 0.988 0.000 0.000
#> GSM152808 3 0.0336 0.9462 0.000 0.000 0.992 0.008
#> GSM152809 2 0.0188 0.9124 0.004 0.996 0.000 0.000
#> GSM152810 4 0.3400 0.6286 0.000 0.000 0.180 0.820
#> GSM152811 3 0.0707 0.9421 0.000 0.000 0.980 0.020
#> GSM152812 2 0.0188 0.9124 0.004 0.996 0.000 0.000
#> GSM152813 2 0.0657 0.9106 0.012 0.984 0.004 0.000
#> GSM152814 2 0.2894 0.8709 0.020 0.900 0.072 0.008
#> GSM152815 2 0.0336 0.9117 0.008 0.992 0.000 0.000
#> GSM152816 3 0.0188 0.9462 0.000 0.000 0.996 0.004
#> GSM152817 3 0.0336 0.9462 0.000 0.000 0.992 0.008
#> GSM152818 3 0.0188 0.9462 0.000 0.000 0.996 0.004
#> GSM152819 3 0.0000 0.9465 0.000 0.000 1.000 0.000
#> GSM152820 3 0.1305 0.9283 0.000 0.004 0.960 0.036
#> GSM152821 2 0.4248 0.7285 0.000 0.768 0.220 0.012
#> GSM153115 2 0.2011 0.8715 0.080 0.920 0.000 0.000
#> GSM153116 3 0.0188 0.9462 0.000 0.000 0.996 0.004
#> GSM153117 3 0.0000 0.9465 0.000 0.000 1.000 0.000
#> GSM153118 2 0.2921 0.8228 0.000 0.860 0.140 0.000
#> GSM153119 3 0.0707 0.9403 0.000 0.000 0.980 0.020
#> GSM153120 2 0.0188 0.9124 0.004 0.996 0.000 0.000
#> GSM153121 3 0.0000 0.9465 0.000 0.000 1.000 0.000
#> GSM153122 3 0.0188 0.9460 0.000 0.000 0.996 0.004
#> GSM153123 2 0.1824 0.8842 0.004 0.936 0.060 0.000
#> GSM153124 2 0.0376 0.9127 0.004 0.992 0.004 0.000
#> GSM153125 2 0.0336 0.9117 0.008 0.992 0.000 0.000
#> GSM153126 3 0.0336 0.9462 0.000 0.000 0.992 0.008
#> GSM153127 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM153128 4 0.5163 0.0406 0.000 0.004 0.480 0.516
#> GSM153129 3 0.1557 0.8999 0.000 0.056 0.944 0.000
#> GSM153130 3 0.0188 0.9462 0.000 0.000 0.996 0.004
#> GSM153131 3 0.0000 0.9465 0.000 0.000 1.000 0.000
#> GSM153132 3 0.0524 0.9435 0.000 0.008 0.988 0.004
#> GSM153133 2 0.3196 0.8227 0.000 0.856 0.136 0.008
#> GSM153134 3 0.1994 0.8967 0.004 0.052 0.936 0.008
#> GSM153135 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM153136 2 0.0188 0.9124 0.004 0.996 0.000 0.000
#> GSM153137 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM153138 2 0.0895 0.9062 0.000 0.976 0.004 0.020
#> GSM153139 3 0.0188 0.9462 0.000 0.000 0.996 0.004
#> GSM153140 2 0.0804 0.9099 0.012 0.980 0.008 0.000
#> GSM153141 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM153142 3 0.0336 0.9449 0.000 0.000 0.992 0.008
#> GSM153143 2 0.0188 0.9121 0.000 0.996 0.000 0.004
#> GSM153144 2 0.1940 0.8730 0.000 0.924 0.076 0.000
#> GSM153145 3 0.0188 0.9460 0.000 0.000 0.996 0.004
#> GSM153146 2 0.3743 0.7948 0.000 0.824 0.160 0.016
#> GSM153147 3 0.5161 0.2710 0.000 0.400 0.592 0.008
#> GSM153148 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM153149 2 0.5161 0.3918 0.000 0.592 0.400 0.008
#> GSM153150 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM153151 2 0.6327 0.5926 0.000 0.648 0.228 0.124
#> GSM153152 3 0.1557 0.9009 0.000 0.056 0.944 0.000
#> GSM153153 2 0.4103 0.6930 0.000 0.744 0.256 0.000
#> GSM153154 3 0.0672 0.9421 0.000 0.008 0.984 0.008
#> GSM153155 2 0.0376 0.9113 0.000 0.992 0.004 0.004
#> GSM153156 3 0.0779 0.9407 0.000 0.004 0.980 0.016
#> GSM153157 3 0.0921 0.9354 0.000 0.000 0.972 0.028
#> GSM153158 3 0.0188 0.9460 0.000 0.000 0.996 0.004
#> GSM153159 3 0.0188 0.9460 0.000 0.000 0.996 0.004
#> GSM153160 3 0.0336 0.9451 0.000 0.000 0.992 0.008
#> GSM153161 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM153162 3 0.0712 0.9414 0.004 0.004 0.984 0.008
#> GSM153163 3 0.0524 0.9431 0.004 0.000 0.988 0.008
#> GSM153164 3 0.3311 0.7393 0.000 0.172 0.828 0.000
#> GSM153165 3 0.0336 0.9451 0.000 0.000 0.992 0.008
#> GSM153166 3 0.2334 0.8592 0.000 0.088 0.908 0.004
#> GSM153167 2 0.4605 0.5621 0.000 0.664 0.336 0.000
#> GSM153168 3 0.0336 0.9462 0.000 0.000 0.992 0.008
#> GSM153169 3 0.0188 0.9460 0.000 0.000 0.996 0.004
#> GSM153170 3 0.0188 0.9462 0.000 0.000 0.996 0.004
#> GSM153171 2 0.0469 0.9109 0.012 0.988 0.000 0.000
#> GSM153172 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM153173 3 0.0188 0.9462 0.000 0.000 0.996 0.004
#> GSM153174 2 0.3219 0.7997 0.000 0.836 0.164 0.000
#> GSM153175 2 0.0188 0.9124 0.004 0.996 0.000 0.000
#> GSM153176 3 0.0188 0.9462 0.000 0.000 0.996 0.004
#> GSM153177 3 0.1902 0.8879 0.000 0.064 0.932 0.004
#> GSM152931 2 0.0707 0.9077 0.020 0.980 0.000 0.000
#> GSM152932 2 0.4608 0.6188 0.004 0.692 0.304 0.000
#> GSM152933 2 0.4103 0.6923 0.000 0.744 0.256 0.000
#> GSM152934 4 0.1398 0.7198 0.000 0.040 0.004 0.956
#> GSM152935 3 0.4817 0.3228 0.000 0.388 0.612 0.000
#> GSM152936 2 0.0188 0.9121 0.000 0.996 0.000 0.004
#> GSM152937 4 0.4252 0.5539 0.000 0.004 0.252 0.744
#> GSM152938 3 0.0000 0.9465 0.000 0.000 1.000 0.000
#> GSM152939 2 0.0469 0.9107 0.012 0.988 0.000 0.000
#> GSM152940 2 0.0188 0.9124 0.004 0.996 0.000 0.000
#> GSM152941 1 0.5050 0.2151 0.588 0.004 0.000 0.408
#> GSM152942 3 0.0188 0.9462 0.000 0.000 0.996 0.004
#> GSM152943 2 0.4655 0.6030 0.000 0.684 0.004 0.312
#> GSM152944 3 0.0000 0.9465 0.000 0.000 1.000 0.000
#> GSM152945 2 0.0376 0.9113 0.000 0.992 0.004 0.004
#> GSM152946 2 0.1584 0.8975 0.012 0.952 0.036 0.000
#> GSM152947 2 0.0707 0.9067 0.020 0.980 0.000 0.000
#> GSM152948 2 0.0188 0.9124 0.004 0.996 0.000 0.000
#> GSM152949 3 0.0376 0.9451 0.000 0.004 0.992 0.004
#> GSM152950 3 0.1042 0.9364 0.000 0.008 0.972 0.020
#> GSM152951 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM152952 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM152953 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM152954 2 0.0188 0.9121 0.000 0.996 0.000 0.004
#> GSM152955 3 0.5256 0.2931 0.000 0.392 0.596 0.012
#> GSM152956 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM152957 2 0.4546 0.7211 0.028 0.780 0.004 0.188
#> GSM152958 2 0.0188 0.9124 0.004 0.996 0.000 0.000
#> GSM152959 4 0.1888 0.7272 0.016 0.044 0.000 0.940
#> GSM152960 2 0.5070 0.3089 0.000 0.580 0.004 0.416
#> GSM152961 2 0.2081 0.8624 0.084 0.916 0.000 0.000
#> GSM152962 3 0.2775 0.8730 0.000 0.020 0.896 0.084
#> GSM152963 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM152964 4 0.3726 0.6050 0.000 0.000 0.212 0.788
#> GSM152965 2 0.3749 0.8177 0.000 0.840 0.128 0.032
#> GSM152966 2 0.0188 0.9124 0.004 0.996 0.000 0.000
#> GSM152967 2 0.0188 0.9124 0.000 0.996 0.004 0.000
#> GSM152968 3 0.0672 0.9421 0.000 0.008 0.984 0.008
#> GSM152969 2 0.0188 0.9124 0.004 0.996 0.000 0.000
#> GSM152970 2 0.4655 0.6948 0.208 0.760 0.000 0.032
#> GSM152971 2 0.0188 0.9124 0.004 0.996 0.000 0.000
#> GSM152972 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM152973 1 0.5296 -0.0322 0.500 0.000 0.492 0.008
#> GSM152974 2 0.3356 0.7871 0.000 0.824 0.176 0.000
#> GSM152975 2 0.3306 0.8076 0.004 0.840 0.156 0.000
#> GSM152976 1 0.2665 0.7604 0.900 0.004 0.088 0.008
#> GSM152977 4 0.3225 0.7195 0.016 0.032 0.060 0.892
#> GSM152978 2 0.0376 0.9123 0.004 0.992 0.000 0.004
#> GSM152979 3 0.0188 0.9462 0.000 0.000 0.996 0.004
#> GSM152980 2 0.1004 0.9045 0.000 0.972 0.004 0.024
#> GSM152981 3 0.1489 0.9222 0.000 0.004 0.952 0.044
#> GSM152982 2 0.2714 0.8418 0.000 0.884 0.004 0.112
#> GSM152983 2 0.0000 0.9127 0.000 1.000 0.000 0.000
#> GSM152984 2 0.2281 0.8591 0.000 0.904 0.096 0.000
#> GSM152985 4 0.4908 0.4899 0.016 0.292 0.000 0.692
#> GSM152986 2 0.0336 0.9117 0.008 0.992 0.000 0.000
#> GSM152987 4 0.4585 0.5224 0.332 0.000 0.000 0.668
#> GSM152988 2 0.0657 0.9106 0.012 0.984 0.004 0.000
#> GSM152989 4 0.2408 0.7414 0.104 0.000 0.000 0.896
#> GSM152990 3 0.0188 0.9462 0.000 0.000 0.996 0.004
#> GSM152991 3 0.0779 0.9407 0.000 0.004 0.980 0.016
#> GSM187524 4 0.1867 0.7434 0.072 0.000 0.000 0.928
#> GSM187525 4 0.4008 0.6552 0.244 0.000 0.000 0.756
#> GSM187526 4 0.4222 0.6195 0.272 0.000 0.000 0.728
#> GSM187527 1 0.0000 0.8797 1.000 0.000 0.000 0.000
#> GSM152856 1 0.0000 0.8797 1.000 0.000 0.000 0.000
#> GSM152857 1 0.1042 0.8598 0.972 0.000 0.020 0.008
#> GSM152858 4 0.3649 0.6931 0.204 0.000 0.000 0.796
#> GSM152859 4 0.0707 0.7336 0.020 0.000 0.000 0.980
#> GSM152860 4 0.3219 0.7179 0.164 0.000 0.000 0.836
#> GSM152861 1 0.3074 0.7647 0.848 0.000 0.000 0.152
#> GSM152862 4 0.2011 0.7436 0.080 0.000 0.000 0.920
#> GSM152863 1 0.2216 0.8256 0.908 0.000 0.000 0.092
#> GSM152864 1 0.0707 0.8792 0.980 0.000 0.000 0.020
#> GSM152865 1 0.3610 0.7029 0.800 0.000 0.000 0.200
#> GSM152866 1 0.3907 0.6535 0.768 0.000 0.000 0.232
#> GSM152867 1 0.0336 0.8819 0.992 0.000 0.000 0.008
#> GSM152868 1 0.0336 0.8817 0.992 0.000 0.000 0.008
#> GSM152869 1 0.0707 0.8792 0.980 0.000 0.000 0.020
#> GSM152870 4 0.2469 0.7402 0.108 0.000 0.000 0.892
#> GSM152871 4 0.4999 0.0823 0.492 0.000 0.000 0.508
#> GSM152872 4 0.3726 0.6864 0.212 0.000 0.000 0.788
#> GSM152873 1 0.0336 0.8819 0.992 0.000 0.000 0.008
#> GSM152874 1 0.0336 0.8819 0.992 0.000 0.000 0.008
#> GSM152875 1 0.0469 0.8818 0.988 0.000 0.000 0.012
#> GSM152876 1 0.0188 0.8774 0.996 0.000 0.000 0.004
#> GSM152877 1 0.0469 0.8818 0.988 0.000 0.000 0.012
#> GSM152878 1 0.0000 0.8797 1.000 0.000 0.000 0.000
#> GSM152879 1 0.0188 0.8810 0.996 0.000 0.000 0.004
#> GSM152880 1 0.0592 0.8808 0.984 0.000 0.000 0.016
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> GSM152804 2 0.5440 0.29502 0.000 0.540 0.396 0.000 0.064
#> GSM152805 3 0.1768 0.74943 0.004 0.000 0.924 0.000 0.072
#> GSM152806 3 0.2011 0.73967 0.004 0.000 0.908 0.000 0.088
#> GSM152807 2 0.3367 0.78081 0.012 0.856 0.052 0.000 0.080
#> GSM152808 3 0.2806 0.69591 0.004 0.000 0.844 0.000 0.152
#> GSM152809 2 0.2388 0.77776 0.012 0.904 0.004 0.004 0.076
#> GSM152810 5 0.5764 0.58267 0.000 0.000 0.152 0.236 0.612
#> GSM152811 3 0.4238 0.34328 0.004 0.000 0.628 0.000 0.368
#> GSM152812 2 0.2291 0.78327 0.008 0.916 0.016 0.004 0.056
#> GSM152813 2 0.3644 0.75485 0.000 0.824 0.096 0.000 0.080
#> GSM152814 2 0.5433 0.56118 0.004 0.640 0.268 0.000 0.088
#> GSM152815 2 0.2478 0.77501 0.008 0.904 0.060 0.000 0.028
#> GSM152816 3 0.2304 0.76414 0.000 0.020 0.908 0.004 0.068
#> GSM152817 3 0.2848 0.69257 0.004 0.000 0.840 0.000 0.156
#> GSM152818 3 0.2124 0.73807 0.004 0.000 0.900 0.000 0.096
#> GSM152819 3 0.2597 0.76069 0.000 0.092 0.884 0.000 0.024
#> GSM152820 3 0.5304 0.26764 0.000 0.056 0.560 0.000 0.384
#> GSM152821 2 0.3684 0.71509 0.000 0.824 0.116 0.004 0.056
#> GSM153115 2 0.5543 0.68844 0.064 0.680 0.020 0.008 0.228
#> GSM153116 3 0.2074 0.77513 0.000 0.036 0.920 0.000 0.044
#> GSM153117 3 0.2966 0.73131 0.000 0.136 0.848 0.000 0.016
#> GSM153118 2 0.3684 0.68252 0.000 0.788 0.192 0.004 0.016
#> GSM153119 3 0.2648 0.70584 0.000 0.000 0.848 0.000 0.152
#> GSM153120 2 0.4335 0.70193 0.036 0.740 0.000 0.004 0.220
#> GSM153121 3 0.2511 0.75724 0.000 0.088 0.892 0.004 0.016
#> GSM153122 3 0.2127 0.73238 0.000 0.000 0.892 0.000 0.108
#> GSM153123 2 0.4585 0.63755 0.000 0.728 0.216 0.004 0.052
#> GSM153124 2 0.5365 0.73738 0.000 0.704 0.104 0.020 0.172
#> GSM153125 2 0.3209 0.74520 0.008 0.812 0.000 0.000 0.180
#> GSM153126 3 0.1121 0.76150 0.000 0.000 0.956 0.000 0.044
#> GSM153127 2 0.1211 0.77866 0.000 0.960 0.016 0.000 0.024
#> GSM153128 5 0.6757 0.51972 0.000 0.024 0.304 0.160 0.512
#> GSM153129 3 0.3733 0.68880 0.000 0.160 0.804 0.004 0.032
#> GSM153130 3 0.0703 0.76890 0.000 0.000 0.976 0.000 0.024
#> GSM153131 3 0.3086 0.74759 0.000 0.092 0.864 0.004 0.040
#> GSM153132 3 0.2813 0.76435 0.000 0.084 0.880 0.004 0.032
#> GSM153133 2 0.2853 0.75228 0.000 0.880 0.076 0.004 0.040
#> GSM153134 3 0.4407 0.65660 0.000 0.172 0.760 0.004 0.064
#> GSM153135 2 0.0898 0.77914 0.000 0.972 0.020 0.000 0.008
#> GSM153136 2 0.3492 0.73668 0.016 0.796 0.000 0.000 0.188
#> GSM153137 2 0.1569 0.78156 0.000 0.944 0.008 0.004 0.044
#> GSM153138 2 0.2654 0.77426 0.000 0.896 0.040 0.008 0.056
#> GSM153139 3 0.0932 0.77108 0.000 0.004 0.972 0.004 0.020
#> GSM153140 2 0.5003 0.71509 0.000 0.720 0.140 0.004 0.136
#> GSM153141 2 0.0898 0.78085 0.000 0.972 0.020 0.000 0.008
#> GSM153142 3 0.2280 0.73060 0.000 0.000 0.880 0.000 0.120
#> GSM153143 2 0.2124 0.77001 0.000 0.900 0.004 0.000 0.096
#> GSM153144 2 0.3606 0.70325 0.000 0.808 0.164 0.004 0.024
#> GSM153145 3 0.2329 0.72377 0.000 0.000 0.876 0.000 0.124
#> GSM153146 2 0.3574 0.73244 0.000 0.836 0.072 0.004 0.088
#> GSM153147 2 0.5980 0.32626 0.000 0.576 0.292 0.004 0.128
#> GSM153148 2 0.1668 0.77456 0.000 0.940 0.032 0.000 0.028
#> GSM153149 2 0.4659 0.63706 0.000 0.744 0.168 0.004 0.084
#> GSM153150 2 0.3612 0.72129 0.008 0.764 0.000 0.000 0.228
#> GSM153151 2 0.6439 -0.09265 0.000 0.456 0.096 0.024 0.424
#> GSM153152 3 0.4996 0.52338 0.000 0.280 0.664 0.004 0.052
#> GSM153153 2 0.4142 0.61545 0.000 0.728 0.252 0.004 0.016
#> GSM153154 3 0.3304 0.76061 0.000 0.092 0.852 0.004 0.052
#> GSM153155 2 0.2172 0.77177 0.000 0.908 0.016 0.000 0.076
#> GSM153156 3 0.2835 0.76358 0.000 0.036 0.880 0.004 0.080
#> GSM153157 3 0.3210 0.63987 0.000 0.000 0.788 0.000 0.212
#> GSM153158 3 0.2370 0.77222 0.000 0.040 0.904 0.000 0.056
#> GSM153159 3 0.1908 0.74448 0.000 0.000 0.908 0.000 0.092
#> GSM153160 3 0.1662 0.76263 0.004 0.004 0.936 0.000 0.056
#> GSM153161 2 0.0703 0.78071 0.000 0.976 0.000 0.000 0.024
#> GSM153162 3 0.3339 0.72506 0.000 0.124 0.836 0.000 0.040
#> GSM153163 3 0.1731 0.76262 0.004 0.004 0.932 0.000 0.060
#> GSM153164 3 0.4655 0.37500 0.000 0.384 0.600 0.004 0.012
#> GSM153165 3 0.2214 0.76645 0.004 0.028 0.916 0.000 0.052
#> GSM153166 3 0.4423 0.60138 0.000 0.232 0.728 0.004 0.036
#> GSM153167 2 0.4512 0.55345 0.000 0.676 0.300 0.004 0.020
#> GSM153168 3 0.2629 0.70663 0.004 0.000 0.860 0.000 0.136
#> GSM153169 3 0.1043 0.76473 0.000 0.000 0.960 0.000 0.040
#> GSM153170 3 0.2142 0.76986 0.000 0.048 0.920 0.004 0.028
#> GSM153171 2 0.4403 0.72673 0.020 0.744 0.008 0.008 0.220
#> GSM153172 2 0.2787 0.76045 0.000 0.880 0.088 0.004 0.028
#> GSM153173 3 0.1216 0.77404 0.000 0.020 0.960 0.000 0.020
#> GSM153174 2 0.3670 0.69335 0.000 0.796 0.180 0.004 0.020
#> GSM153175 2 0.4395 0.74045 0.004 0.752 0.020 0.016 0.208
#> GSM153176 3 0.5949 0.39078 0.012 0.000 0.632 0.180 0.176
#> GSM153177 3 0.4165 0.63627 0.000 0.208 0.756 0.004 0.032
#> GSM152931 2 0.4747 0.70266 0.084 0.720 0.000 0.000 0.196
#> GSM152932 2 0.5412 0.15245 0.000 0.520 0.428 0.004 0.048
#> GSM152933 2 0.3421 0.70034 0.000 0.816 0.164 0.004 0.016
#> GSM152934 5 0.5971 0.42511 0.000 0.112 0.008 0.300 0.580
#> GSM152935 3 0.4974 0.00678 0.000 0.488 0.488 0.004 0.020
#> GSM152936 2 0.2966 0.74160 0.000 0.816 0.000 0.000 0.184
#> GSM152937 5 0.6502 0.59952 0.000 0.020 0.160 0.260 0.560
#> GSM152938 3 0.2913 0.75360 0.000 0.080 0.876 0.004 0.040
#> GSM152939 2 0.3779 0.74068 0.024 0.776 0.000 0.000 0.200
#> GSM152940 2 0.3177 0.73573 0.000 0.792 0.000 0.000 0.208
#> GSM152941 4 0.5055 0.65329 0.168 0.004 0.000 0.712 0.116
#> GSM152942 3 0.1630 0.77131 0.000 0.016 0.944 0.004 0.036
#> GSM152943 2 0.5628 0.56224 0.000 0.660 0.016 0.100 0.224
#> GSM152944 3 0.0955 0.76837 0.000 0.004 0.968 0.000 0.028
#> GSM152945 2 0.1818 0.77348 0.000 0.932 0.024 0.000 0.044
#> GSM152946 2 0.5738 0.57775 0.000 0.644 0.228 0.012 0.116
#> GSM152947 2 0.3883 0.72482 0.016 0.764 0.000 0.004 0.216
#> GSM152948 2 0.1918 0.78136 0.000 0.928 0.036 0.000 0.036
#> GSM152949 3 0.2919 0.74758 0.000 0.104 0.868 0.004 0.024
#> GSM152950 3 0.4499 0.69418 0.000 0.136 0.764 0.004 0.096
#> GSM152951 2 0.2878 0.77112 0.000 0.880 0.068 0.004 0.048
#> GSM152952 2 0.1018 0.77847 0.000 0.968 0.016 0.000 0.016
#> GSM152953 2 0.0865 0.77859 0.000 0.972 0.024 0.000 0.004
#> GSM152954 2 0.3366 0.73355 0.000 0.784 0.000 0.004 0.212
#> GSM152955 3 0.6820 -0.12600 0.000 0.336 0.416 0.004 0.244
#> GSM152956 2 0.0703 0.78069 0.000 0.976 0.000 0.000 0.024
#> GSM152957 4 0.6547 0.42078 0.036 0.196 0.012 0.624 0.132
#> GSM152958 2 0.3353 0.73469 0.008 0.796 0.000 0.000 0.196
#> GSM152959 4 0.6031 0.11508 0.000 0.244 0.000 0.576 0.180
#> GSM152960 2 0.5920 0.39992 0.000 0.588 0.000 0.160 0.252
#> GSM152961 2 0.6565 0.44581 0.252 0.536 0.000 0.012 0.200
#> GSM152962 5 0.6666 0.24712 0.000 0.128 0.368 0.024 0.480
#> GSM152963 2 0.1281 0.77887 0.000 0.956 0.012 0.000 0.032
#> GSM152964 5 0.6407 0.57164 0.000 0.000 0.204 0.296 0.500
#> GSM152965 2 0.4880 0.61878 0.000 0.728 0.060 0.016 0.196
#> GSM152966 2 0.3282 0.74082 0.008 0.804 0.000 0.000 0.188
#> GSM152967 2 0.1356 0.77864 0.000 0.956 0.028 0.004 0.012
#> GSM152968 3 0.3854 0.74303 0.000 0.100 0.816 0.004 0.080
#> GSM152969 2 0.2891 0.74535 0.000 0.824 0.000 0.000 0.176
#> GSM152970 4 0.7461 0.24385 0.080 0.312 0.000 0.464 0.144
#> GSM152971 2 0.3550 0.73512 0.020 0.796 0.000 0.000 0.184
#> GSM152972 2 0.2966 0.74036 0.000 0.816 0.000 0.000 0.184
#> GSM152973 3 0.6145 0.52844 0.092 0.036 0.668 0.016 0.188
#> GSM152974 2 0.4774 0.55673 0.000 0.680 0.276 0.004 0.040
#> GSM152975 2 0.4818 0.72096 0.000 0.720 0.180 0.000 0.100
#> GSM152976 3 0.8089 0.06827 0.180 0.012 0.460 0.108 0.240
#> GSM152977 5 0.5042 0.47107 0.008 0.028 0.036 0.200 0.728
#> GSM152978 2 0.3143 0.73520 0.000 0.796 0.000 0.000 0.204
#> GSM152979 3 0.2075 0.77030 0.000 0.032 0.924 0.004 0.040
#> GSM152980 2 0.2277 0.77406 0.000 0.916 0.016 0.016 0.052
#> GSM152981 3 0.4448 -0.01679 0.000 0.000 0.516 0.004 0.480
#> GSM152982 2 0.5167 0.62687 0.000 0.664 0.000 0.088 0.248
#> GSM152983 2 0.3353 0.73735 0.008 0.796 0.000 0.000 0.196
#> GSM152984 2 0.5612 0.68265 0.004 0.668 0.168 0.004 0.156
#> GSM152985 5 0.7034 -0.01634 0.016 0.376 0.000 0.216 0.392
#> GSM152986 2 0.4392 0.71404 0.048 0.748 0.000 0.004 0.200
#> GSM152987 4 0.3759 0.72397 0.136 0.000 0.000 0.808 0.056
#> GSM152988 2 0.4585 0.73684 0.004 0.728 0.052 0.000 0.216
#> GSM152989 4 0.3248 0.70135 0.052 0.004 0.000 0.856 0.088
#> GSM152990 3 0.2751 0.76034 0.000 0.056 0.888 0.004 0.052
#> GSM152991 3 0.4065 0.55381 0.000 0.016 0.720 0.000 0.264
#> GSM187524 4 0.3359 0.68526 0.072 0.000 0.000 0.844 0.084
#> GSM187525 4 0.2753 0.72982 0.136 0.000 0.000 0.856 0.008
#> GSM187526 4 0.3123 0.71487 0.160 0.000 0.000 0.828 0.012
#> GSM187527 1 0.1124 0.88241 0.960 0.000 0.000 0.036 0.004
#> GSM152856 1 0.1018 0.85990 0.968 0.000 0.000 0.016 0.016
#> GSM152857 1 0.3319 0.81147 0.864 0.000 0.064 0.052 0.020
#> GSM152858 4 0.2932 0.73670 0.104 0.000 0.000 0.864 0.032
#> GSM152859 4 0.2719 0.56352 0.004 0.000 0.000 0.852 0.144
#> GSM152860 4 0.2136 0.74060 0.088 0.000 0.000 0.904 0.008
#> GSM152861 4 0.4268 0.16963 0.444 0.000 0.000 0.556 0.000
#> GSM152862 4 0.2079 0.72371 0.064 0.000 0.000 0.916 0.020
#> GSM152863 1 0.4101 0.43090 0.628 0.000 0.000 0.372 0.000
#> GSM152864 1 0.3534 0.69323 0.744 0.000 0.000 0.256 0.000
#> GSM152865 4 0.4306 -0.01662 0.492 0.000 0.000 0.508 0.000
#> GSM152866 1 0.3461 0.74085 0.772 0.000 0.000 0.224 0.004
#> GSM152867 1 0.2377 0.84706 0.872 0.000 0.000 0.128 0.000
#> GSM152868 1 0.2605 0.83259 0.852 0.000 0.000 0.148 0.000
#> GSM152869 1 0.2648 0.82954 0.848 0.000 0.000 0.152 0.000
#> GSM152870 4 0.2104 0.72373 0.060 0.000 0.000 0.916 0.024
#> GSM152871 4 0.4486 0.66962 0.172 0.000 0.000 0.748 0.080
#> GSM152872 4 0.3002 0.73334 0.116 0.000 0.000 0.856 0.028
#> GSM152873 1 0.0671 0.88047 0.980 0.000 0.000 0.016 0.004
#> GSM152874 1 0.0609 0.88253 0.980 0.000 0.000 0.020 0.000
#> GSM152875 1 0.1671 0.87423 0.924 0.000 0.000 0.076 0.000
#> GSM152876 1 0.0451 0.86415 0.988 0.000 0.000 0.008 0.004
#> GSM152877 1 0.0963 0.88353 0.964 0.000 0.000 0.036 0.000
#> GSM152878 1 0.0162 0.87483 0.996 0.000 0.000 0.004 0.000
#> GSM152879 1 0.0771 0.88222 0.976 0.000 0.000 0.020 0.004
#> GSM152880 1 0.0865 0.88264 0.972 0.000 0.000 0.024 0.004
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> GSM152804 2 0.5326 0.35563 0.000 0.536 0.372 0.084 0.004 0.004
#> GSM152805 3 0.1562 0.67377 0.000 0.004 0.940 0.024 0.032 0.000
#> GSM152806 3 0.1049 0.66976 0.000 0.000 0.960 0.008 0.032 0.000
#> GSM152807 2 0.3530 0.59285 0.004 0.780 0.004 0.196 0.012 0.004
#> GSM152808 3 0.2404 0.61228 0.000 0.000 0.872 0.016 0.112 0.000
#> GSM152809 2 0.3437 0.56271 0.004 0.788 0.000 0.188 0.012 0.008
#> GSM152810 5 0.3271 0.59286 0.000 0.004 0.144 0.004 0.820 0.028
#> GSM152811 3 0.4204 -0.21897 0.000 0.004 0.540 0.008 0.448 0.000
#> GSM152812 2 0.2261 0.68154 0.000 0.884 0.000 0.104 0.004 0.008
#> GSM152813 2 0.4087 0.65383 0.000 0.764 0.044 0.168 0.024 0.000
#> GSM152814 2 0.5284 0.66019 0.004 0.688 0.124 0.152 0.028 0.004
#> GSM152815 2 0.2501 0.70963 0.004 0.892 0.012 0.076 0.012 0.004
#> GSM152816 3 0.3205 0.67901 0.000 0.060 0.852 0.028 0.060 0.000
#> GSM152817 3 0.2538 0.59849 0.000 0.000 0.860 0.016 0.124 0.000
#> GSM152818 3 0.1391 0.66689 0.000 0.000 0.944 0.016 0.040 0.000
#> GSM152819 3 0.4109 0.47751 0.000 0.328 0.652 0.008 0.012 0.000
#> GSM152820 5 0.6082 0.20153 0.000 0.224 0.356 0.004 0.416 0.000
#> GSM152821 2 0.2520 0.73012 0.000 0.888 0.068 0.012 0.032 0.000
#> GSM153115 4 0.4724 0.75539 0.016 0.188 0.004 0.712 0.080 0.000
#> GSM153116 3 0.3561 0.64285 0.000 0.160 0.796 0.012 0.032 0.000
#> GSM153117 2 0.4450 0.09523 0.000 0.528 0.448 0.004 0.020 0.000
#> GSM153118 2 0.2695 0.71216 0.000 0.844 0.144 0.008 0.004 0.000
#> GSM153119 3 0.3122 0.58870 0.000 0.020 0.816 0.004 0.160 0.000
#> GSM153120 4 0.5241 0.74058 0.008 0.304 0.000 0.608 0.068 0.012
#> GSM153121 3 0.4120 0.54313 0.000 0.276 0.692 0.008 0.024 0.000
#> GSM153122 3 0.1788 0.65434 0.000 0.004 0.916 0.004 0.076 0.000
#> GSM153123 2 0.3822 0.68641 0.000 0.772 0.180 0.032 0.016 0.000
#> GSM153124 4 0.5050 0.70153 0.000 0.276 0.036 0.648 0.032 0.008
#> GSM153125 4 0.3722 0.78164 0.004 0.260 0.000 0.724 0.004 0.008
#> GSM153126 3 0.1932 0.68132 0.000 0.016 0.924 0.020 0.040 0.000
#> GSM153127 2 0.2162 0.70698 0.004 0.896 0.000 0.088 0.012 0.000
#> GSM153128 5 0.7364 0.59932 0.000 0.120 0.260 0.044 0.480 0.096
#> GSM153129 3 0.4217 0.55834 0.000 0.260 0.700 0.016 0.024 0.000
#> GSM153130 3 0.0881 0.69081 0.000 0.012 0.972 0.008 0.008 0.000
#> GSM153131 3 0.4060 0.62910 0.000 0.180 0.760 0.028 0.032 0.000
#> GSM153132 3 0.4435 0.40874 0.000 0.364 0.604 0.004 0.028 0.000
#> GSM153133 2 0.1592 0.73023 0.000 0.940 0.020 0.008 0.032 0.000
#> GSM153134 3 0.4753 0.35034 0.000 0.380 0.576 0.028 0.016 0.000
#> GSM153135 2 0.1956 0.71300 0.004 0.908 0.000 0.080 0.008 0.000
#> GSM153136 4 0.4288 0.78656 0.016 0.256 0.000 0.704 0.012 0.012
#> GSM153137 2 0.3349 0.49098 0.000 0.748 0.000 0.244 0.008 0.000
#> GSM153138 2 0.4235 0.58998 0.000 0.740 0.028 0.204 0.024 0.004
#> GSM153139 3 0.0622 0.69149 0.000 0.012 0.980 0.000 0.008 0.000
#> GSM153140 4 0.6226 0.46773 0.000 0.356 0.116 0.480 0.048 0.000
#> GSM153141 2 0.2256 0.69163 0.004 0.892 0.000 0.092 0.008 0.004
#> GSM153142 3 0.2615 0.65279 0.000 0.028 0.876 0.008 0.088 0.000
#> GSM153143 2 0.3025 0.60748 0.000 0.820 0.000 0.156 0.024 0.000
#> GSM153144 2 0.2896 0.72969 0.000 0.864 0.080 0.044 0.012 0.000
#> GSM153145 3 0.1701 0.64821 0.000 0.000 0.920 0.008 0.072 0.000
#> GSM153146 2 0.2515 0.72025 0.000 0.888 0.024 0.016 0.072 0.000
#> GSM153147 2 0.4302 0.63405 0.000 0.728 0.116 0.000 0.156 0.000
#> GSM153148 2 0.0993 0.71874 0.000 0.964 0.000 0.024 0.012 0.000
#> GSM153149 2 0.3139 0.70828 0.000 0.848 0.084 0.012 0.056 0.000
#> GSM153150 4 0.4701 0.75597 0.004 0.292 0.000 0.652 0.040 0.012
#> GSM153151 2 0.4807 0.54516 0.000 0.696 0.052 0.028 0.220 0.004
#> GSM153152 2 0.3993 0.49913 0.000 0.676 0.300 0.000 0.024 0.000
#> GSM153153 2 0.2531 0.71567 0.000 0.860 0.128 0.004 0.008 0.000
#> GSM153154 3 0.4681 0.20534 0.000 0.432 0.524 0.000 0.044 0.000
#> GSM153155 2 0.2119 0.70002 0.000 0.904 0.000 0.060 0.036 0.000
#> GSM153156 3 0.4297 0.56398 0.000 0.204 0.728 0.012 0.056 0.000
#> GSM153157 3 0.3288 0.56668 0.000 0.016 0.800 0.008 0.176 0.000
#> GSM153158 3 0.3419 0.62724 0.000 0.176 0.792 0.004 0.028 0.000
#> GSM153159 3 0.1901 0.68037 0.000 0.028 0.924 0.008 0.040 0.000
#> GSM153160 3 0.2171 0.67895 0.000 0.016 0.912 0.040 0.032 0.000
#> GSM153161 2 0.1845 0.69828 0.004 0.916 0.000 0.072 0.008 0.000
#> GSM153162 3 0.5366 0.25662 0.000 0.404 0.516 0.052 0.028 0.000
#> GSM153163 3 0.2024 0.68198 0.000 0.016 0.920 0.028 0.036 0.000
#> GSM153164 2 0.3670 0.53754 0.000 0.704 0.284 0.000 0.012 0.000
#> GSM153165 3 0.2803 0.68825 0.000 0.064 0.876 0.032 0.028 0.000
#> GSM153166 2 0.3996 0.31888 0.000 0.604 0.388 0.004 0.004 0.000
#> GSM153167 2 0.4333 0.65567 0.000 0.720 0.200 0.076 0.004 0.000
#> GSM153168 3 0.2263 0.62443 0.000 0.000 0.884 0.016 0.100 0.000
#> GSM153169 3 0.1700 0.69283 0.000 0.028 0.936 0.012 0.024 0.000
#> GSM153170 3 0.2633 0.68703 0.000 0.104 0.864 0.032 0.000 0.000
#> GSM153171 4 0.3683 0.78140 0.000 0.192 0.000 0.764 0.044 0.000
#> GSM153172 2 0.2704 0.71106 0.000 0.868 0.020 0.100 0.012 0.000
#> GSM153173 3 0.1745 0.69744 0.000 0.056 0.924 0.020 0.000 0.000
#> GSM153174 2 0.3079 0.72708 0.000 0.848 0.092 0.052 0.008 0.000
#> GSM153175 4 0.3309 0.78827 0.000 0.192 0.000 0.788 0.016 0.004
#> GSM153176 3 0.6573 0.17810 0.000 0.008 0.572 0.164 0.108 0.148
#> GSM153177 2 0.4165 0.22003 0.000 0.568 0.420 0.004 0.008 0.000
#> GSM152931 4 0.4452 0.77577 0.044 0.204 0.000 0.728 0.016 0.008
#> GSM152932 2 0.3947 0.57449 0.000 0.716 0.256 0.016 0.012 0.000
#> GSM152933 2 0.2615 0.71990 0.000 0.852 0.136 0.004 0.008 0.000
#> GSM152934 5 0.4369 0.45508 0.000 0.040 0.008 0.060 0.776 0.116
#> GSM152935 2 0.3897 0.49226 0.000 0.684 0.300 0.008 0.008 0.000
#> GSM152936 4 0.4350 0.76316 0.000 0.280 0.000 0.676 0.036 0.008
#> GSM152937 5 0.6296 0.58697 0.000 0.088 0.104 0.036 0.636 0.136
#> GSM152938 3 0.3440 0.67191 0.000 0.108 0.828 0.028 0.036 0.000
#> GSM152939 4 0.4500 0.73313 0.020 0.272 0.000 0.680 0.024 0.004
#> GSM152940 4 0.4035 0.78064 0.000 0.272 0.000 0.700 0.016 0.012
#> GSM152941 6 0.5007 0.39604 0.044 0.008 0.000 0.404 0.004 0.540
#> GSM152942 3 0.2891 0.66932 0.000 0.032 0.872 0.060 0.036 0.000
#> GSM152943 2 0.6614 0.00326 0.000 0.448 0.000 0.240 0.272 0.040
#> GSM152944 3 0.1333 0.69611 0.000 0.048 0.944 0.000 0.008 0.000
#> GSM152945 2 0.1909 0.71060 0.000 0.920 0.004 0.052 0.024 0.000
#> GSM152946 2 0.5846 0.52398 0.000 0.592 0.172 0.204 0.032 0.000
#> GSM152947 4 0.2845 0.78493 0.004 0.172 0.000 0.820 0.000 0.004
#> GSM152948 2 0.2519 0.66920 0.000 0.864 0.004 0.124 0.004 0.004
#> GSM152949 3 0.4350 0.24764 0.000 0.428 0.552 0.004 0.016 0.000
#> GSM152950 2 0.5004 0.11634 0.000 0.516 0.420 0.004 0.060 0.000
#> GSM152951 2 0.3168 0.66755 0.000 0.820 0.028 0.148 0.004 0.000
#> GSM152952 2 0.1333 0.71152 0.000 0.944 0.000 0.048 0.008 0.000
#> GSM152953 2 0.1152 0.71511 0.000 0.952 0.000 0.044 0.004 0.000
#> GSM152954 4 0.3988 0.76689 0.004 0.260 0.000 0.712 0.020 0.004
#> GSM152955 3 0.7262 -0.30304 0.000 0.156 0.380 0.320 0.144 0.000
#> GSM152956 2 0.2121 0.68070 0.000 0.892 0.000 0.096 0.012 0.000
#> GSM152957 4 0.5575 -0.14855 0.008 0.048 0.004 0.468 0.020 0.452
#> GSM152958 4 0.3925 0.78652 0.004 0.260 0.000 0.716 0.012 0.008
#> GSM152959 4 0.6247 0.32184 0.000 0.076 0.000 0.528 0.096 0.300
#> GSM152960 2 0.6978 -0.29917 0.000 0.340 0.000 0.284 0.320 0.056
#> GSM152961 4 0.4819 0.76884 0.084 0.168 0.000 0.720 0.016 0.012
#> GSM152962 2 0.6501 -0.21202 0.000 0.392 0.284 0.020 0.304 0.000
#> GSM152963 2 0.1370 0.71224 0.004 0.948 0.000 0.036 0.012 0.000
#> GSM152964 5 0.7014 0.56032 0.000 0.032 0.236 0.044 0.492 0.196
#> GSM152965 2 0.2981 0.69654 0.000 0.848 0.016 0.020 0.116 0.000
#> GSM152966 4 0.3678 0.78536 0.008 0.228 0.000 0.748 0.016 0.000
#> GSM152967 2 0.2723 0.68894 0.000 0.852 0.000 0.128 0.016 0.004
#> GSM152968 3 0.4955 0.22094 0.000 0.420 0.520 0.004 0.056 0.000
#> GSM152969 4 0.3337 0.78337 0.000 0.260 0.000 0.736 0.004 0.000
#> GSM152970 4 0.5856 0.26627 0.028 0.056 0.004 0.584 0.024 0.304
#> GSM152971 4 0.4401 0.77933 0.020 0.280 0.000 0.680 0.008 0.012
#> GSM152972 4 0.4204 0.76815 0.004 0.296 0.000 0.676 0.012 0.012
#> GSM152973 3 0.7083 0.21046 0.028 0.032 0.548 0.220 0.132 0.040
#> GSM152974 2 0.3321 0.68721 0.000 0.796 0.180 0.016 0.008 0.000
#> GSM152975 4 0.6050 0.55962 0.000 0.296 0.172 0.512 0.020 0.000
#> GSM152976 4 0.6473 0.11871 0.028 0.012 0.288 0.556 0.080 0.036
#> GSM152977 4 0.4885 0.31221 0.000 0.000 0.040 0.556 0.392 0.012
#> GSM152978 4 0.4484 0.74284 0.000 0.320 0.000 0.640 0.028 0.012
#> GSM152979 3 0.2867 0.68729 0.000 0.064 0.872 0.024 0.040 0.000
#> GSM152980 2 0.3229 0.63139 0.000 0.828 0.000 0.120 0.048 0.004
#> GSM152981 5 0.4151 0.42566 0.000 0.004 0.412 0.008 0.576 0.000
#> GSM152982 4 0.5841 0.55156 0.000 0.104 0.008 0.548 0.320 0.020
#> GSM152983 4 0.3161 0.79210 0.000 0.216 0.000 0.776 0.008 0.000
#> GSM152984 4 0.5099 0.66594 0.004 0.236 0.056 0.672 0.028 0.004
#> GSM152985 4 0.4980 0.64295 0.000 0.084 0.000 0.684 0.204 0.028
#> GSM152986 4 0.3925 0.79436 0.024 0.220 0.000 0.744 0.004 0.008
#> GSM152987 6 0.4315 0.63489 0.040 0.000 0.000 0.244 0.012 0.704
#> GSM152988 4 0.4300 0.73841 0.008 0.184 0.008 0.752 0.040 0.008
#> GSM152989 6 0.4702 0.45115 0.016 0.000 0.000 0.388 0.024 0.572
#> GSM152990 3 0.3677 0.67075 0.000 0.104 0.816 0.040 0.040 0.000
#> GSM152991 3 0.4967 0.39079 0.000 0.108 0.644 0.004 0.244 0.000
#> GSM187524 6 0.3897 0.71902 0.040 0.000 0.000 0.048 0.112 0.800
#> GSM187525 6 0.3159 0.75475 0.056 0.000 0.000 0.056 0.032 0.856
#> GSM187526 6 0.3463 0.75000 0.080 0.000 0.000 0.064 0.024 0.832
#> GSM187527 1 0.0547 0.88709 0.980 0.000 0.000 0.000 0.000 0.020
#> GSM152856 1 0.0291 0.87578 0.992 0.000 0.000 0.004 0.000 0.004
#> GSM152857 1 0.2554 0.83605 0.876 0.000 0.076 0.000 0.000 0.048
#> GSM152858 6 0.1605 0.76453 0.032 0.000 0.000 0.016 0.012 0.940
#> GSM152859 6 0.3594 0.66746 0.008 0.000 0.000 0.028 0.184 0.780
#> GSM152860 6 0.1700 0.76508 0.028 0.000 0.000 0.012 0.024 0.936
#> GSM152861 6 0.4004 0.28468 0.368 0.000 0.000 0.012 0.000 0.620
#> GSM152862 6 0.1599 0.76365 0.024 0.000 0.000 0.008 0.028 0.940
#> GSM152863 1 0.4024 0.41112 0.592 0.000 0.000 0.004 0.004 0.400
#> GSM152864 1 0.3421 0.71858 0.736 0.000 0.000 0.008 0.000 0.256
#> GSM152865 6 0.4536 -0.11903 0.476 0.000 0.000 0.024 0.004 0.496
#> GSM152866 1 0.3281 0.78426 0.784 0.000 0.000 0.012 0.004 0.200
#> GSM152867 1 0.2278 0.85788 0.868 0.000 0.000 0.004 0.000 0.128
#> GSM152868 1 0.2442 0.84821 0.852 0.000 0.000 0.004 0.000 0.144
#> GSM152869 1 0.2915 0.81285 0.808 0.000 0.000 0.008 0.000 0.184
#> GSM152870 6 0.1546 0.76179 0.020 0.000 0.000 0.016 0.020 0.944
#> GSM152871 6 0.2847 0.74803 0.040 0.000 0.000 0.036 0.048 0.876
#> GSM152872 6 0.1605 0.76489 0.032 0.000 0.000 0.012 0.016 0.940
#> GSM152873 1 0.0632 0.89095 0.976 0.000 0.000 0.000 0.000 0.024
#> GSM152874 1 0.0547 0.89038 0.980 0.000 0.000 0.000 0.000 0.020
#> GSM152875 1 0.1556 0.88160 0.920 0.000 0.000 0.000 0.000 0.080
#> GSM152876 1 0.0146 0.87891 0.996 0.000 0.000 0.000 0.000 0.004
#> GSM152877 1 0.0937 0.89090 0.960 0.000 0.000 0.000 0.000 0.040
#> GSM152878 1 0.0000 0.88134 1.000 0.000 0.000 0.000 0.000 0.000
#> GSM152879 1 0.0458 0.88923 0.984 0.000 0.000 0.000 0.000 0.016
#> GSM152880 1 0.0713 0.89128 0.972 0.000 0.000 0.000 0.000 0.028
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
As soon as we have had the classes for columns, we can look for signatures which are significantly different between classes which can be candidate marks for certain classes. Following are the heatmaps for signatures.
Signature heatmaps where rows are scaled:
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
Signature heatmaps where rows are not scaled:
get_signatures(res, k = 2, scale_rows = FALSE)
get_signatures(res, k = 3, scale_rows = FALSE)
get_signatures(res, k = 4, scale_rows = FALSE)
get_signatures(res, k = 5, scale_rows = FALSE)
get_signatures(res, k = 6, scale_rows = FALSE)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. TO get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows.UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
Test correlation between subgroups and known annotations. If the known annotation is numeric, one-way ANOVA test is applied, and if the known annotation is discrete, chi-squared contingency table test is applied.
test_to_known_factors(res)
#> n tissue(p) k
#> ATC:NMF 167 1.35e-18 2
#> ATC:NMF 164 1.15e-24 3
#> ATC:NMF 161 2.19e-25 4
#> ATC:NMF 147 4.47e-22 5
#> ATC:NMF 134 3.76e-22 6
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
sessionInfo()
#> R version 3.6.0 (2019-04-26)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS: /usr/lib64/libblas.so.3.4.2
#> LAPACK: /usr/lib64/liblapack.so.3.4.2
#>
#> locale:
#> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8
#> [4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
#> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] grid stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] genefilter_1.66.0 ComplexHeatmap_2.3.1 markdown_1.1 knitr_1.26
#> [5] GetoptLong_0.1.7 cola_1.3.2
#>
#> loaded via a namespace (and not attached):
#> [1] circlize_0.4.8 shape_1.4.4 xfun_0.11 slam_0.1-46
#> [5] lattice_0.20-38 splines_3.6.0 colorspace_1.4-1 vctrs_0.2.0
#> [9] stats4_3.6.0 blob_1.2.0 XML_3.98-1.20 survival_2.44-1.1
#> [13] rlang_0.4.2 pillar_1.4.2 DBI_1.0.0 BiocGenerics_0.30.0
#> [17] bit64_0.9-7 RColorBrewer_1.1-2 matrixStats_0.55.0 stringr_1.4.0
#> [21] GlobalOptions_0.1.1 evaluate_0.14 memoise_1.1.0 Biobase_2.44.0
#> [25] IRanges_2.18.3 parallel_3.6.0 AnnotationDbi_1.46.1 highr_0.8
#> [29] Rcpp_1.0.3 xtable_1.8-4 backports_1.1.5 S4Vectors_0.22.1
#> [33] annotate_1.62.0 skmeans_0.2-11 bit_1.1-14 microbenchmark_1.4-7
#> [37] brew_1.0-6 impute_1.58.0 rjson_0.2.20 png_0.1-7
#> [41] digest_0.6.23 stringi_1.4.3 polyclip_1.10-0 clue_0.3-57
#> [45] tools_3.6.0 bitops_1.0-6 magrittr_1.5 eulerr_6.0.0
#> [49] RCurl_1.95-4.12 RSQLite_2.1.4 tibble_2.1.3 cluster_2.1.0
#> [53] crayon_1.3.4 pkgconfig_2.0.3 zeallot_0.1.0 Matrix_1.2-17
#> [57] xml2_1.2.2 httr_1.4.1 R6_2.4.1 mclust_5.4.5
#> [61] compiler_3.6.0