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Table 2 Type I error rate for seven algorithms

From: Comparisons of seven algorithms for pathway analysis using the WTCCC Crohn's Disease dataset

Algorithms

Type I error

(0.05)

K-S test

(two-sided)

GATES-Simes

0.043

< 2.2e-12

GATES-Hyper

0.016

5.4e-09

Aligator

0.032

2.6e-3

GRASS

0.018

5.1e-12

GSEAforGWAS

0.016

< 2.2e-16

PLINK-Ave

0.055

3.1e-06

PLINK-Max

0.036

9.5e-05

  1. Two indices (Type I error and K-S test) were used to check whether those algorithms produced more false positive results than by chance. Type I error was calculated as proportion of pathways with nominal p-values < 0.05. The two-sided Kolmogorov-Smirnov test was used to investigate whether p-values from each algorithm follow the theoretical (0, 1) uniform distribution.
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BMC Research Notes

ISSN: 1756-0500

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