Dear BioC, I have a pretty straight two-color microarray question. My data is in .gpr format, which I have attempted to normalize using the limma and limmaGUI packages in R. My output for each array consists of one value per gene scaled to zero for BOTH CY3 and CY5 combined. Is this expected? I had anticipated my output would consist of separate values for each dye and that they would be log2 fold intensities (similar to single color arrays). I have not been able to find much info regarding this. Any insight will be greatly appreciated. Thanks, Bryan [[alternative HTML version deleted]]