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It is pretty unclear to me what you are trying to accomplish. The RMA procedure consists of background subtraction (on a per chip level), quantile normalization (all chips together, probe level) and summarization. Are you talking about quantile normalization? And do you then want to do this on the probeset level instead of the probe level? Kasper On May 4, 2007, at 8:35 AM, James Anderson wrote: > > I am now trying to get the probe level values from RMA, since I > want to adjust > the batch effect in probe level instead of probe set level. However, > justRMA seems to do everything until the probe set level. What I > want to do > is to use RMA to obtain probe level expression matrix, then adjust > the batch > effect, then using median polish to get probe set level. > Does anybody know how to circumvent the memory problem if > I only want to get the probe level matrix? > > Many thanks, > > James > > > --------------------------------- > > > [[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

Hi James, James Anderson wrote: > I am now trying to get the probe level values from RMA, since I want to adjust > the batch effect in probe level instead of probe set level. However, > justRMA seems to do everything until the probe set level. What I want to do > is to use RMA to obtain probe level expression matrix, then adjust the batch > effect, then using median polish to get probe set level. > Does anybody know how to circumvent the memory problem if > I only want to get the probe level matrix? Why exactly do you want to adjust for batch at the probe level? The batch effect will be a per-chip effect, so I wouldn't imagine that adjusting at the probe level would be that much different, except for the fact that you would be doing things pre-medianpolish, so any outliers could really skew things. Anyway, if you are limited by RAM I don't think you will be able to do really fancy things. I would recommend either increasing the amount of RAM you have, or finding a computer that has enough. If you want to do probe-level modeling you should be using the affyPLM package which IIRC doesn't have any methods explicitly designed to use minimal amounts of RAM. Best, Jim > > Many thanks, > > James > > > --------------------------------- > > > [[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.