Software
All statistical analysis, method implementation, and graphing for figures, was performed using the open-source programming language R, Versions 2.0.1 – 2.4.0 [26], and Bioconductor packages . Affymetrix® CEL files were processed using the MAS 5.0 and RMA algorithms implemented in the BioConductor package: affy Version 1.5.8 [27] (based on the R programming language) and by dChip® 2006 (Build date: Feb. 16, 2006). Gene Set Enrichment Analysis (GSEA) was performed using the author's R language implementation version GSEA.1.0.R [25].