Statistical analysis of the CeA samples incorporated a ‘batch effect’, which prevented an analysis of the individual time points. In addition, correcting for a batch effect allowed us to use a more critical FDR value for the CeA than was used for the ACB-shell. Setting the maximum FDR at 0.10, there were 1,156 probe sets that were significantly different between the ethanol and water groups, with 754 probe sets for ESTs and 402 probe sets for named genes being different (Table 1). There were 384 unique named genes that were significantly different in the CeA between water and ethanol groups (see Supplemental Table C for a complete list of significantly different probe sets in the CeA). There were 1.5-fold more individual named genes that had higher expression than lower expression levels in the ethanol group compared to the water control group (Table 1).
