Table 2 Average number of shared differentially expressed genes found by different methods for the CMAP dataset (FDR ≤ 10%)
From: Influence of batch effect correction methods on drug induced differential gene expression profiles
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) |