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Table 2 Number of detected DE genes using different single study analysis methods (PT, RIM_ALL, RIM_minP and RIM_BIC) in the five individual studies and by two meta-analysis methods (Fisher and maxP)

From: Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: With application to major depressive disorder

method FDR Individual analysis Meta-analysis
(3ACC+2AMY)
   MD1_ACC MD2_ACC MD3_ACC MD1_AMY MD3_AMY Fisher maxP
RIM_minP FDR = 0.05 0 0 2 0 0 0 0
  FDR = 0.1 0 0 2 0 725 109 99
  FDR = 0.15 0 0 5 0 1442 810 683
RIM_BIC FDR = 0.05 0 0 0 0 101 0 0
  FDR = 0.1 0 0 1 0 506 0 0
  FDR = 0.15 0 0 6 0 873 38 0
RIM_ALL FDR = 0.05 0 0 0 0 0 0 1
  FDR = 0.1 0 3 0 0 1 0 1
  FDR = 0.15 0 3 1 0 1 0 1
PT FDR = 0.05 0 0 0 0 0 0 0
  FDR = 0.1 0 0 0 0 0 0 0
  FDR = 0.15 1 1 0 0 0 0 0
  1. Three FDR thresholds are used (5%, 10% and 15%)