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Table 6 Comparing gene set analysis methods performance under the null hypothesis simulated by class labels permutation

From: Down-weighting overlapping genes improves gene set analysis

  p median Rank median % p.value<0.05
PADOG 0.49 48.9 4.9
GSA 0.51 50.6 5.3
GSEA 0.50 50.1 5.0
  1. The medians of target pathways p-values and ranks, as well as the fraction of target pathways with p<0.05 were computed in 100 simulation trials. At each trial the class labels of the samples in each of 24 real datasets were permuted before analysis. The averages statistics over the 100 trials are shown.