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Table 2 Type I error of different methods

From: Pathway-based analysis using reduced gene subsets in genome-wide association studies

Methods

TNFR2 Signaling Pathway (pattern 1)

Fructose and mannose metabolism (pattern 2)

Cytokine-cytokine receptor interaction (pattern 3)

 

Type I error (95% CI)

P-value

Type I error (95% CI)

P-value

Type I error (95% CI)

P-value

FPC_AIC

0.060 (0.039,0.081)

0.302

0.058 (0.038,0.078)

0.326

0.054 (0.034,0.074)

0.653

FPC_BIC

0.050 (0.031,0.069) NA

0.048 (0.029,0.067) NA

0.048 (0.029,0.067) NA

FPC_FULL

0.058 (0.038,0.078)

0.492

0.054 (0.034,0.074)

0.673

0.048 (0.029,0.067)

0.932

AML

0.062 (0.041,0.083)

0.346

0.042 (0.024,0.060)

0.653

0.034 (0.018,0.050)

0.285

MSS

0.058 (0.038,0.078)

0.523

0.050 (0.031,0.069)

0.933

0.042 (0.024,0.060)

0.689

RTP_5

0.058 (0.038,0.078)

0.536

0.046 (0.028,0.064)

0.917

0.042 (0.024,0.060)

0.673

RTP_10

0.064 (0.043,0.085)

0.258

0.048 (0.029,0.067)

0.922

0.044 (0.026,0.062)

0.797

  1. For each of the methods, we presented the type I error, the 95% confidence interval of all estimated probabilities, the p-value of McNemar's test for the difference of type I error between FPC_BIC and other methods. The type I error was calculated on the basis of 500 replicates at significance level 0.05.