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Hi Max, MaximilianOtto at gmx.at wrote: > Dear list, My question may be quite basic and it concerns the rma > algorithm for affy data. As the idea behind rma is to take into > account the between array variance for a probe set to calculate an > expression value, I'm not sure if I can run rma on a set of cel files > representing different conditions - for example have 2 conditions, > each replicated 3 times - 6 arrays total. should rma be run for all 6 > arrays or for each of three separately. in extreme I may have > non-replicated experiments - use rma or not? Any suggestions are > greatly appreciated! Thanks Max You almost always want to run RMA on all chips at one time. Even when you are doing different conditions, most of the genes are not differentially expressed (at least that is the assumption most normalization schemes use). In addition, RMA is based on the idea that the pattern of probe intensities for a given probeset will be similar over different conditions, but the overall intensity may change. In other words, RMA is designed to account for similarities in the probe intensity pattern (likely non-Biological) while still detecting overall intensity differences. Therefore, the expectation is that the data given to RMA will contain different conditions that you are planning on comparing. That said, QA of the raw data is essential. RMA isn't magic, and if your data don't conform to the assumptions, the results you get will likely not be ideal. The affyQCReport package is one way to check the quality of your raw data. Best, Jim > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.