Hello all, I need to normalize expression array from command line using a specific array as baseline median array. Does anybody know a package that allows me to do that? I have checked the expresso package and think that it does not allow me to specify a specific array as median array. Thanks and have great holiday! AG Lee [[alternative HTML version deleted]]

Hi, aroma.affymetrix can do this: library("aroma.affymetrix"); csR <- AffymetrixCelSet$byName("MyDataSet", chipType="HG- U133_Plus_2"); cfT <- getFile(csR, 14); # Normalize toward array #14 (say) qn <- QuantileNormalization(csR, targetDistribution=cfT); csN <- process(qn); For further question, please join the aroma.affymetrix mailinglist [http://www.braju.com/R/aroma.affymetrix/]. Cheers Henrik On Wed, Dec 24, 2008 at 4:15 PM, Li, Aiguo (NIH/NCI) [E] <liai at="" mail.nih.gov=""> wrote: > Hello all, > > > > I need to normalize expression array from command line using a specific > array as baseline median array. Does anybody know a package that allows > me to do that? I have checked the expresso package and think that it > does not allow me to specify a specific array as median array. > > > > Thanks and have great holiday! > > > > AG Lee > > > [[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 >