Hello, For a factorial design with some replicates at each level one could assume that the replicates within each level are more similar to each other than across levels (or even factors, especially if the factor is something like "patient" or "animal"). One could normalize within the replicates 1st and then a 2nd round of normalizaton across the factor levels. Would this make sense (at all)? Has anybody tried this with bioC methods such as rma+quantile? I'd be interested in your comments about this topic. kind regards, Arne -- Arne Muller, Ph.D. Toxicogenomics, Aventis Pharma arne dot muller domain=aventis com

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