Table 3

Type 1 error of different pathway enrichment methods

Pattern number

A

SEPEA_NT1

GSEA

Maxmean

SEPEA_NT2

SEPEA_NT3


1

0.01

8

5

85

13

135

0.05

36

51

187

44

266

5

0.01

7

12

12

7

15

0.05

51

45

48

52

53


Type 1 errors (in terms of the number of experiments out of 1,000 that gave P-values for the randomization tests below α = 0.01 and 0.05 levels) for each of the five methods and for correlation patterns 1 and 5.

Thomas et al. Genome Biology 2009 10:R44   doi:10.1186/gb-2009-10-4-r44

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