Gene expression levels were extracted and summarized from the 9 Affymetrix CEL files using the MG-Mm430 Ensembl Custom CDF file (version 10) based on mouse Ensembl genes. We used the Rma algorithm (R-Bioconductor “affy” package) for background correction and quantile normalization of log2 transformed expression levels. Genes with expression levels above background were determined based on the Wilcoxon test, with the “mas5” function (R-Bioconductor “affy” package) and a cutoff of p<0.05. Among the 15,758 Ensembl genes present on the array, 12,198 were detectable with this criterion in at least one array and these were further analyzed. Student’s t-test was used to compare gene expression levels between the 9 samples.
