Hi guys, I wonder if anyone is able to provide some directions for this. I have a total of about 34 arrays that are hybridized to the Affymetrix Human Exon ST1.0 arrays. After performing a differential gene expression analysis using limma, I wonder if there is any way for me to detect possible gene-gene interactions- based on the results from limma? Some ways I looked at are G.O and G.S.E.A (in limma), but I'm not sure if these tests are the best way to look for epistatic effects between genes in a complex disease like asthma. Any suggestions on where I can head? Thanks for any suggestions! Jeremy [[alternative HTML version deleted]]