Micro Array Suite 5.0 (Affymetrix) derived cell intensity files (CEL) were processed in R 2.1.1 language and environment (http://www.R-project.org) using Bioconductor 1.6 packages.47 Each array was inspected for regional hybridization bias and quality control parameters as recently described.48 Fifty-three arrays (27 from caudate putamen and 26 from amygdala) passed the quality filter and were included in the statistical analysis. Of the 8799 probe sets on the RG_U34A array, only those with intensity values > 100 in at least 25 % of the samples were retained (6344 probe sets). A 3-way ANOVA was used to identify differentially expressed genes across strain, brain region and treatment. The list of genes affected by long-term ethanol consumption included those with a p < 0.05 for treatment from the 3-way ANOVA. Posthoc analysis was performed via template matching across strains. Correlation coefficients (r) for consistent up or down regulation by ethanol in either caudate putamen or amygdala or both regions were calculated.
