The association analyses above were carried out with individual transcripts, identified by Affymetrix or Illumina probes. In order to facilitate comparison between platforms, we next analyzed the results at the level of individual genes, identified by the Affymetrix or Illumina annotation. We defined that a gene was associated with an eSNP if any probe belonging to the gene was significantly (FDR < 5%) associated with the SNP. We note that Illumina and Affymetrix probesets annotated to the same gene may target different transcripts of that gene with the possibility of different association results (Veyrieras et al. 2012).
