Hello, I have searched in the FAQ and mailing list, but cannot find an answer to my question. I apologize if this has been asked before. I have a series of hybs using a long-oligo spotted array for maize, and am using two-color (Cy3 & Cy5-labelled) targets. I would like to generate a list of probes that detect signal that is 'above background' for each target - that would be, significantly greater than signal detected by the negative control probes on the array (Aliens and Human sequences). These would hopefully identify a set of genes that are expressed vs not-detectably-expressed in my tissues of interest. I have a loop design, and am using limma to identify differentially expressed genes. Is it possible to use limma to also do the analysis I suggested above? I assume that this would involve using the separate channel functions of limma, but am unclear on how to approach it. Many thanks, John -- John Fowler Associate Professor Botany and Plant Pathology (BPP) Dept. 2082 Cordley Hall Phone: (541) 737-5307 Oregon State University FAX: (541) 737-3573 Corvallis, OR 97331-2902 USA Email: fowlerj at science.oregonstate.edu