Hi all, I have a question about working with ratios in SAM analysis. I have 8 CEL files, C1,C2...C8 in one AffyBatch file, called CEL.Batch and I would like to do the two class (unpaired) SAM analysis between two groups of ratios: group1: C1/C2 and C3/C4 (duplicates) group2: C5/C6 and C7/C8 (duplicates), How can I get the ratio of two columns of an AffyBatch file? and how to make the result acceptable to SAM? Any suggestion would be greatly appreciated. Fan