4.0 in both alcoholics and controls were removed. The remaining probe sets were analyzed using a 3-way ANOVA with the factors of phenotype (control/alcoholic), sex (male/female), and processing batch (for potential technical variations). Interaction between sex and phenotype was not significant after correcting for multiple testing (Storey & Tibshirani, 2003) and was removed from the analysis. Fold changes were calculated using the untransformed RMA signals. False discovery rates (FDR) were calculated using q-value (Storey & Tibshirani, 2003).
