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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.