Hi group, I'm trying to preprocess some two-colours single-channel slides. Looking through the mailing list archives I found some suggestions. But I still have some doubts... 1) first of all, a very basic question. In our group we came to the decision to simply don't consider the second channel (green) and to make all the work (BGcorrect, norm, etc) on the only one used (red). Is it right ? 2) Looking at the background images we found a clear block effect, and also a kind of gradient through the three subarrays we have for each slide. Do you is possible/useful try to remove this effect with a linear model (I mean a simple lm(signal~block) or lm(signal~block+ row + col...) , or there are already correction methods in BioC that can be efficiently applied for these purposes (both, the block effect mainly but the gradient to) ? Which ones ? Thanks a lot in advance, Regards Giulio _________________________________________________________________ Windows Live OneCare: tutto per la cura del tuo PC ! Provalo Gratis!