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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)
  1. Abbreviations: ASS = Average signature size (removed missing values)
  2. 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