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Table 2 Estimated false discovery rate (FDR) of null hypotheses using different combinations of the three groups

From: Correspondence regarding "Effect of active smoking on the human bronchial epithelium transcriptome"

  null dataset actual dataset  
null hypothesis ≥20 TPM p ≤ 0.05 fold-change ≥ 2 ≥20 TPM p ≤ 0.05 fold-change ≥ 2 FDR
N = C 7406 418 195 7764 885 609 47.2
N = F 7323 384 157 7547 765 447 50.2
F = C 7102 416 92 7318 895 433 46.5
(N, F) = C 7726 411 82 8148 959 460 42.8
N = (F, C) 7726 382 67 8148 836 475 45.7
(N, C) = F 7726 388 157 8148 818 314 47.4
  1. The estimated false discovery rate (FDR) of different null hypotheses when grouping the 24 SAGE libraries of Chari et al. into never, former, and current smokers. A p-value cutoff of 0.05 was used, as in the original paper.