GeneChips® for both of these experiments were processed in The Center for Medical Genomics at Indiana University School of Medicine. Affymetrix Microarray Suite 5.0 was used to generate signal values and detection calls and the data were exported for further analysis. Both of these data sets were globally scaled to a target of 1000; default parameters were used for the detection call algorithm. We also used the R package "Affy", which is part of the Bioconductor Project [23], to calculate an alternate measure of expression level using the default parameters for the robust multichip average (RMA) algorithm [17,18].
