mRNA expression data was collected on the Affymetrix human GeneChip HGU133 Plus 2.0 array and normalized using the RMA method [55] without background correction (i.e. quantile normalization followed by robust probe-set summarization). All expression data (from all abdominal and gluteal samples) were preprocessed together. Publicly available custom chip-definition files (CDFs) were downloaded (version 9) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp) and used to group probes into sets, each set corresponding to an Ensembl-annotated gene, resulting 17,209 such genes represented in the array data. See Dai et al [56] for a description of how these CDFs were created, along with a comparison of their properties with the CDFs produced by Affymetrix.
