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Table 1 Estimated type I error rates for simulation 1 with varying number of random effects

From: Permutation-based variance component test in generalized linear mixed model with application to multilocus genetic association study

n

Method

K

20

30

40

400

Permutation

0.046

0.055

0.054

 

Score

0.043

0.045

0.048

 

Mixture (0.50)

0.016

0.020

0.021

 

Mixture (0.65)

0.020

0.026

0.027

600

Permutation

0.052

0.047

0.044

 

Score

0.045

0.042

0.037

 

Mixture (0.50)

0.016

0.016

0.013

 

Mixture (0.65)

0.020

0.021

0.017

800

Permutation

0.052

0.054

0.051

 

Score

0.048

0.052

0.047

 

Mixture (0.50)

0.014

0.015

0.012

 

Mixture (0.65)

0.020

0.019

0.020

1000

Permutation

0.051

0.041

0.053

 

Score

0.050

0.036

0.051

 

Mixture (0.50)

0.017

0.014

0.011

 

Mixture (0.65)

0.020

0.017

0.017

  1. Note: Permutation is the proposed permutation-based LRT, Score is the score-based sequence kernel association test given in Wu, et al. [31] that was originally developed in Lin (1997), Mixture(0.50) and Mixture (0.65) respectively correspond to the asymptotic 0.50:0.50 and 0.65:035 mixtures of chi-square distributions. Here K is the number of random effects, i.e., the number of SNPs included in a gene.
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BMC Medical Research Methodology

ISSN: 1471-2288

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