Jake: Sport fans might like dangerous waters. 8-) To the topic, I have anecdotal evidence that glass-slide array can actually be one-color, if your printing quality is very good. With such a high quality array, I did not see any difference by sticking to R/G ratios, or treat them the single-channel way. Simon >>I was wondering (thinking of this from the single-channel mentality) if >>there's a way to use marray (or another package) to get normalized >>intensities of each channel, rather than log-ratios; this would >>essentially treat each channel like an individual single-channel chip. >>Somebody please stop me in my tracks if I'm heading into dangerous >>waters by using a single-channel mentality with two-color chips! > > You are heading in very dangerous waters indeed and, almost certainly, you > don't really want to do it. If you change your technology, you need to > change you thinking as well. The red-green pairing is the whole point of > the two-colour technology and you cannot ignore it without drastic loss of > accuracy.