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Table 3 Impact of choice of gene set statistics on detecting gene set enrichment.

From: A general modular framework for gene set enrichment analysis

 

mean

maxmean

median

ES

cond. FDR

Wilcoxon

set 1

0.67

0.67

0.82

0.56

0.68

0.84

set 2

0.92

0.93

0.98

0.65

0.94

1.00

set 3

0.01

0.01

0.00

0.00

0.01

0.01

set 4

0.44

0.45

0.57

0.35

0.45

0.54

set 5

0.41

0.41

0.32

0.22

0.42

0.41

set 6

0.85

0.86

0.94

0.80

0.85

0.96

set 7

1.00

1.00

1.00

0.99

1.00

1.00

set 8

0.70

0.71

0.78

0.65

0.84

0.74

set 9

0.90

0.86

0.81

0.69

0.99

0.80

  1. The indicated values correspond to the proportion of p-values ≤ 0.05 for squared moderated t and resampling.