Hi, when we calcuate the expression values, we'd like to get rid of the affy control genes (AFFX-xxx genes). Shoud we do it before we call RMA or expresso function, or after. I don't know how to do it. Do the RMA and expresso functions already exclude those genes from affybatch when they do the calculations? If not, how can I get a new affybatch object withont AFFX genes from the old affybatch (from ReadAffy() ). Thanks in advance, Linlin Chen =========================== Linlin Chen lchen@bst.rochester.edu