In our current dataset (12 samples) we compared human male and female gene expression levels on Affymetrix U95A chips using a model based expression analysis (Li and Wong, PNAS, 2001,98 (1),31-36). We replicated the findings of gender differences in gene expression (Evans, S. et al., SFN abstract this meeting). Our findings using a model based approach agreed with the Evans et al. findings on 4 of the 6 highest gene expression differences in which they used absolute Affymetrix calls as filtering criteria in pair wise comparisons between a larger set of male and female samples. We examined duplicate Affymetrix chips to establish reliability and false positive rates. The chip to chip variation suggested that two criteria were useful to minimize false positive gene expression differences. Thus, we find evidence of gene expression differences between gender that is specific to sex chromosome-linked genes. We have examined gene expression in three brain regions and find that two cortical regions, dorsolateral p...