The large fraction of eQTLs specific to each platform is likely due to their particular designs (Veyrieras et al. 2012). There are 7601 genes queried by at least one probe in both Affymetrix U133 Plus2 and Illumina Human6 V1 chips. Among these, 5625 genes were associated with an eQTL, and 2483 of them were mapped in both MRCA and MRCE (986 genes specific to MRCA and 2156 genes specific to MRCE). These findings are consistent with other studies that suggest that these Affymetrix and Illumina arrays provide complementary information for gene expression (Pedotti et al. 2008).
