Table 2.
Average number of shared differentially expressed genes found by different methods for the CMAP dataset (FDR ≤ 10%)
| Method | limma+Null | limma+1PC | limma+2PCs | limma+3PCs | limma+4PCs | limma+Batch id | LEAPP |
|---|---|---|---|---|---|---|---|
| Limma+Null | (ASS = 50) | 44 (37.3%) | 27 (20.0%) | 18 (14.9%) | 14 (14.1%) | 49 (19.6%) | 9 (11.0%) |
| limma+1PC | 44 (88.0%) | (ASS = 118) | 61 (45.2%) | 39 (32.2%) | 28 (18.2%) | 106 (42.4%) | 15 (18.3%) |
| limma+2PCs | 27 (54.0%) | 61 (51.7%) | (ASS = 135) | 81 (66.9%) | 55 (55.6%) | 120 (48.0%) | 17 (20.7%) |
| limma+3PCs | 18 (36.0%) | 39 (33.1%) | 81 (60.0%) | (ASS = 121) | 70 (70.7%) | 100 (40.0%) | 17 (20.7%) |
| limma+4PCs | 14 (28.0%) | 28 (23.7%) | 55 (40.7%) | 70 (57.9%) | (ASS = 99) | 75 (30.0%) | 15 (18.3%) |
| limma+Batch id | 49 (98.0%) | 106 (89.8%) | 120 (88.9%) | 100 (82.6%) | 75 (75.8%) | (ASS = 250) | 25 (30.5%) |
| LEAPP | 9 (18.0%) | 15 (12.7%) | 17 (12.6%) | 17 (14.0%) | 15 (15.2%) | 25 (10.0%) | (ASS = 82) |
Abbreviations: ASS = Average signature size (removed missing values)
Note: The table contains the number of differentially expressed genes that are shared between each pair of methods on the CMAP dataset. The numbers on the diagonal indicate the average number of differentially expressed genes found by the respective methods. For the LEAPP method, the significant genes with estimate = 0 were ignored. Percentages in parentheses are the proportions of the number of shared genes to average signature size produced by the method on the column header