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Table 1 Mean values of the test statistics (Wald for Linear, score for mmscore), genomic control λ (median test statistic over 0.455), and type 1 error at different α for different models.

From: ProbABEL package for genome-wide association analysis of imputed data

   

α

Model

Mean( T 2 )

λ

0.05

0.01

0.001

Linear

1.206

1.224

0.073

0.018

0.0027

Linear, robust

1.210

1.228

0.073

0.018

0.0028

Linear, mmscore

0.984

1.007

0.047

0.009

0.0011

  1. Tests were performed using a trait dependent on two covariates and with (adjusted) heritability of 30%. Only SNPs with estimated minor allele frequency greater than 0.01 (n = 212, 691) used. Linear: standard linear model; Linear, robust: linear models using with standard errors; Linear, mmscore: two-step approximation to mixed model, fixed effects included in step 1 of analysis.
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BMC Bioinformatics

ISSN: 1471-2105

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