This study attempted to take into consideration (a) the schedule of sacrificing animals by sacrificing water control rats along with each of the time points for the ethanol groups; (b) a cohort effect by conducting the experiments with a single cohort of rats; (c) a batch effect by counterbalancing samples at each step (although this was not completely accomplished with the CeA samples); and (d) number of false positives by placing more emphasis on clustering within GO categories and/or fitting within a pathway analysis. In addition, the KEGG analyses for the ACB-shell and CeA did not add much more information than provided by the GO and Ingenuity analyses. Therefore, the results of the KEGG analyses are not discussed.
