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

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