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Table 4 Comparison of methods for assigning significance.

From: A general modular framework for gene set enrichment analysis

  parametric resampling permutation restandardization
set 1 0.82 0.67 0.59 0.66
set 2 1.00 0.92 1.00 0.92
set 3 0.03 0.01 0.06 0.01
set 4 0.60 0.44 0.51 0.43
set 5 0.85 0.41 0.90 0.41
set 6 0.96 0.85 0.83 0.84
set 7 1.00 1.00 1.00 1.00
set 8 0.90 0.70 0.79 0.68
set 9 0.99 0.90 1.00 0.87
  1. The values indicated are the proportion of p-values ≤ 0.05 using the gene set statistic mean of the individual squared moderated t-statistics.