Figure 1.Compare clustering results. Left panel: The difference score, number of clusters and the block mean of different clusterings. Right panel: Concordance between clustering methods. The concordance measures how similar two clusterings are. The definition of the concordance score can be found here.
Table 1.Number of clusters identified by each clustering method. Numbers in the table indicate the number of clusters. The numbers inside the parentheses are the number of clusters with size >= 5.
| ID | binary_cut | kmeans | pam | dynamicTreeCut | mclust | apcluster | hdbscan | fast_greedy | louvain | walktrap | MCL | Details |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| E-GEOD-13637_A-AFFY-44_g1_g2 | 6(1) | 3(3) | 2(2) | 6(5) | 3(3) | 12(5) | 1(1) | 32(1) | 33(0) | 1(1) | 45(0) | view |
| E-GEOD-13637_A-AFFY-44_g1_g9 | 5(1) | 9(2) | 3(1) | 8(8) | 3(3) | 15(8) | 1(1) | 36(1) | 34(1) | 1(1) | 54(1) | view |
| E-GEOD-13637_A-AFFY-44_g5_g3 | 10(1) | 4(2) | 2(1) | 5(4) | 1(1) | 8(3) | 1(1) | 29(0) | 29(0) | 1(1) | 31(0) | view |
| E-GEOD-1417_A-AFFY-33_g1_g2 | 1(1) | 7(4) | 5(4) | 8(7) | 1(1) | 12(5) | 1(1) | 38(0) | 37(0) | 1(1) | 46(0) | view |
| E-GEOD-16837_A-AFFY-44_g22_g11 | 8(1) | 3(3) | 2(2) | 4(3) | 1(1) | 6(3) | 1(1) | 26(0) | 26(0) | 1(1) | 27(0) | view |
| E-GEOD-16837_A-AFFY-44_g22_g21 | 1(1) | 5(3) | 3(3) | 4(4) | 1(1) | 7(3) | 1(1) | 26(0) | 26(0) | 1(1) | 29(0) | view |
| E-GEOD-16837_A-AFFY-44_g22_g29 | 5(1) | 4(2) | 2(1) | 6(5) | 1(1) | 10(3) | 1(1) | 31(0) | 31(0) | 1(1) | 39(0) | view |
| E-GEOD-19018_A-AFFY-44_g2_g1 | 1(1) | 3(2) | 3(3) | 3(3) | 1(1) | 5(2) | 1(1) | 26(0) | 26(0) | 1(1) | 27(0) | view |
| E-GEOD-24592_A-AFFY-37_g1_g3 | 5(1) | 3(1) | 2(1) | 5(4) | 1(1) | 7(4) | 1(1) | 28(0) | 28(0) | 1(1) | 31(0) | view |
| E-GEOD-44384_g1_g2 | 6(1) | 6(2) | 2(2) | 6(6) | 2(2) | 10(4) | 1(1) | 30(1) | 29(1) | 1(1) | 35(1) | view |
| E-GEOD-46538_A-AFFY-44_g3_g1 | 1(1) | 11(7) | 2(2) | 13(13) | 3(3) | 26(12) | 1(1) | 33(6) | 33(6) | 1(1) | 87(1) | view |
| E-GEOD-50694_A-AFFY-37_g5_g4 | 1(1) | 5(3) | 2(2) | 5(5) | 2(2) | 11(5) | 1(1) | 34(1) | 33(0) | 1(1) | 45(1) | view |
| E-GEOD-51258_A-AFFY-44_g1_g2 | 4(1) | 4(1) | 2(1) | 8(7) | 1(1) | 11(4) | 1(1) | 32(0) | 32(0) | 1(1) | 43(0) | view |
| E-GEOD-56788_g2_g12 | 8(1) | 3(1) | 2(1) | 3(2) | 1(1) | 8(0) | 1(1) | 23(0) | 23(0) | 1(1) | 24(0) | view |
| E-GEOD-57463_A-AFFY-44_g2_g1 | 2(2) | 2(2) | 2(2) | 4(4) | 2(2) | 8(2) | 1(1) | 27(0) | 27(0) | 1(1) | 29(0) | view |
| E-MEXP-1372_A-AFFY-44_g4_g2 | 2(2) | 6(3) | 2(2) | 8(8) | 2(2) | 13(6) | 1(1) | 36(1) | 36(1) | 1(1) | 50(0) | view |
| E-MTAB-3447_g5_g3 | 2(2) | 6(4) | 2(2) | 10(10) | 7(5) | 13(7) | 1(1) | 35(1) | 34(1) | 1(1) | 62(0) | view |
| E-MTAB-3731_A-AFFY-33_g4_g12 | 4(1) | 4(2) | 3(1) | 4(3) | 1(1) | 7(3) | 1(1) | 28(0) | 28(0) | 1(1) | 28(0) | view |
| E-MTAB-4732_g2_g1 | 2(2) | 5(3) | 2(2) | 8(8) | 3(3) | 13(4) | 1(1) | 35(1) | 34(1) | 1(1) | 46(1) | view |
| E-MTAB-6345_g1_g2 | 2(2) | 5(2) | 2(2) | 6(6) | 2(2) | 8(4) | 1(1) | 33(1) | 33(0) | 1(1) | 36(1) | view |
| E-MTAB-6681_g6_g4 | 4(1) | 4(3) | 3(2) | 4(4) | 1(1) | 7(5) | 1(1) | 30(0) | 30(0) | 1(1) | 33(0) | view |
| E-MTAB-7000_g1_g2 | 3(2) | 6(4) | 2(2) | 8(7) | 2(2) | 13(7) | 1(1) | 33(1) | 33(1) | 1(1) | 55(0) | view |
| E-MTAB-7000_g3_g4 | 5(1) | 3(2) | 2(2) | 3(2) | 1(1) | 5(2) | 1(1) | 25(0) | 25(0) | 1(1) | 25(0) | view |
| E-MTAB-8215_g1_g2 | 4(1) | 5(3) | 2(2) | 4(4) | 1(1) | 7(5) | 1(1) | 33(1) | 33(1) | 1(1) | 34(1) | view |