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Table 7 False positive rates when null hypothesis is simulated by generating random expression data

From: Down-weighting overlapping genes improves gene set analysis

  α= 0.05 α= 0.01
PADOG 0.051 0.012
GSA 0.052 0.015
GSEA 0.052 0.012
  1. The fraction of all pathways significant at α=0.05 and α=0.01 were computed after applying the three analysis methods on 1200 datasets having expression data generated from a random normal N(0,1) distribution. The collection of gene sets used in the analysis was defined by the 229 KEGG non-metabolic and metabolic pathways.