of the oligonucleotide probe, SVi..n represents the effects of a matrix of 55 surrogate variables, and e is the residual error. The model was fitted to each gene by residual maximum likelihood using the lmer function in the R package lme4 (v 0.999375-32) [62], [63]. Fixed effect p-values were estimated using the pvals.fnc function in the languageR package (v 1.0) [64]. The significance of covariate effects was assessed by estimating false discovery rates, using Storey's q-value method [65]. To further control for the effects of outliers and population stratification, prior to eQTL mapping, the distribution of estimated individual effects, for each gene expression trait, was normal quantile transformed, within populations.
