hey all, i have several thousand affy arrays from various tissues and various mice...and we are doing a large scale eQTL study and i was wondering if anyone can suggest the best way to normalize/filter the data...i ran justRMA over all of the chips but we are only interested in the biologically active genes in each tissue type...i was thinking about doing a simple baseline filter on the RMA adjusted values for each tissue type...does that sound reasonable? ~j