Hello: Assume that one conservatively expects to see a dye effect in Agilent data for all genes. One should then for example average expression values of corresponding green and red channels in a dye-swapped design. The routine "loess.normalize" in the Affy package does normalization between all pairs of arrays. Assuming there is a dye effect, would it make any sense to use individual red and green channels in this process? Or should one first do dye normalization and then apply pairwise loess normalization? Another intriguing question (at least for me) is whether one should take logs prior to loess normalization. I know why one should usually take logs to do t-test or ANOVA analysis (to make the data look more Gaussian), but it is not clear if this should be done before or after applying loess. Thank you for your time. Ulisses. ---------------------------------------------------------------------- -- Ulisses M. Braga-Neto, Ph.D. Dept. of Electrical and Computer Eng. Assistant Professor Texas A&M University ulisses at ece.tamu.edu Tel: (979) 862-6441 http://www.ece.tamu.edu/~ulisses FAX: (979) 845-6259