used as a cutoff because this allowed a significant number of genes to be included in the Gene Ontology (GO) and Ingenuity® Pathways Analysis to help identify networks of genes that changed. This FDR value is a reasonably stringent cutoff value that provides a good balance between allowing more thorough gene network analyses (limiting beta-error) without including too many false positives (limiting alpha-error) in the analyses. Thus, to facilitate discussion of the present results in the context of our laboratory's previously published work with microarray data (c.f., Edenberg et al., 2005; Kimpel et al., 2007; Rodd et al., 2008), we have used the same standard statistical procedures used previously, and by the field (Gentleman et al., 2004; Irizarry et al., 2003; Smyth, 2004), to determine the effects of the two different ethanol drinking conditions on changes in gene expression.
