Since RNA expression arrays of the 3 sample groups were performed at different times, the correlation between the genotype and expression levels was calculated separately in each sample group to avoid the influences of batch effects. The Pearson’s correlation coefficient (r) between the genotype (coded as 0, 1, or 2) and gene expression level was calculated for each of the 1.63×1010 SNP-expression probe pairs in the 3 sample groups. The correlation coefficients of the 3 sample groups were averaged according to the following equation [19]:
