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Table 3 Results of simulation study: Fisher's exact test.

From: Comparative study of gene set enrichment methods

  α= 0.01 α= 0.02 α= 0.03 α= 0.04 α= 0.05
  P-value P-value P-value P-value P-value
  mean se mean se mean se mean se mean se
1 0.4117 0.0901 0.2789 0.0773 0.1509 0.0411 0.1243 0.0406 0.1137 0.0427
2 0.1961 0.0795 0.0342 0.0171 0.0270 0.0217 0.0287 0.0265 0.0140 0.0120
3 0.0085 0.0033 0.0019 0.0011 0.0024 0.0010 0.0034 0.0020 0.0053 0.0034
4 0.0030 0.0017 0.0016 0.0006 0.0039 0.0018 0.0081 0.0037 0.0113 0.0039
5 2e-04 0.0002 1e-06 0 1e-06 0 6e-07 0 7e-07 0
  1. P-values for the first gene set in the five different scenarios (rows) described in the text. In each column we report the significance level (α) adopted in t-test to find DE genes.