We next filtered out probe sets that were not detectable above background in our samples; this has been shown to reduce noise in microarray experiments (McClintick and Edenberg, 2006). Probe sets that did not have at least 25% of samples with normalized scaled expression greater than 64 were not analyzed. Linear modeling to calculate gene-wise p values for the contrasts of the ethanol group versus water group was performed using the package Limma (Smyth, 2004). Probe sets were considered to be statistically significant at FDR = 0.1 (calculated according to Storey et al., 2004).
