SVA [20] was performed on the matrix of expression measurements, after controlling for the effects of age, sex, and a principal component analysis based quantification of genetic ancestry; 54 significant surrogate variables were identified. For each probeset, we then constructed a linear model y ∼ m + A + C + R + W + SVi..n + e, where y is the log2 transformed probe intensity, m is the expected probe intensity, A is the effect of individual age, and C is the effect of individual sex, and R is the effect of genetic ancestry, W is the effect of the oligonucleotide probe, SVi..n represents the effects of a matrix of surrogate variables, and e is the residual expression. Models were implemented with the lm function in R. The residuals from this regression were used as the phenotype values for all subsequent analyses.
