Hi all, I'm a little more familiar with single-channel chips (Affy) than I am with spotted two-color arrays, and I'm now starting to get involved with the analysis of some two-color arrays. 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. I'd like to then convert these normalized intensities into an exprSet, with two intensities per chip. In other words, if I had 12 two-color chips, I'd like to end up with a 24-column exprSet. Somebody please stop me in my tracks if I'm heading into dangerous waters by using a single-channel mentality with two-color chips! Thanks! --Jake