To integrate the different expression platforms for the purpose of meta-analysis, we developed an empirical probe-matching approach. We used the pruned SNPs to conduct per-platform meta-analyses for all Illumina arrays, for all RNA-seq datasets, and for each Affymetrix dataset separately, using summary statistics from analyses without correction for PCs. For each platform, this yielded an empirical trans-eQTL Z-score matrix, as well as 10 permuted Z-score matrices in which links between genotype and expression files were shuffled. These permuted Z-score matrices reflect the gene–gene or probe–probe correlation structure.
