Hello List, I'm considering alternate means to normalize an Affy Exon array experiment of triplicate arrays over (non) induction of a condition and (non) treatment in-vitro with an exoribonuclease. The same quantity of RNA was selected for each array; however, we expect that there will be some global or nearly global degradation of transcripts to a small degree and many partially degraded transcripts among various of the 4 samples, and I'm looking to identify those transcripts which were partially degraded in one sample compared to another. I don't think RMA is appropriate for this dataset given that there shouldn't be much real up or down regulation; however, there should be some extremely common degradation effects in some of the samples. What normalization approach might be useful here? Sincerely, Brian Kennedy Department of Molecular Cellular Biology The Ohio State University