Hi I wondered what the list felt about calculating ratios between channels from separate microarrays? Let me explain. I have come across an experiment (not designed by myself) where I have the following: +ve cell lines - cell lines with random genomic insertions that display a +ve phenotype -ve cell lines - cell lines with random genomic insertions that display a -ve phenotype Parental cell lines with no genomic insertion Now to me it would have made sense to compare +ve vs parental and -ve vs parental to find those genes which are present in the insertions but not in the parent which may be contributing to the phenotype. However, the experimenter did not do this; they compared each +ve cell line to the -ve cell lines, and also the parental cell lines to the -ve cell lines. So intuitively what I want to do is calculate ratios of +ve/parental and -ve/parental for each of the experiments, when what I have is +ve/-ve and parental/-ve. Is it valid simply to take the (single) list of values for the parental cell line and use that repeatedly as the denominator for the +ve and -ve channels from the other arrays? Thanks Mick