Hi, I've been trying to use PLIER to pre-process microarray data from 5 Rat 230A chips. After using the justPlier function, I get an exprSet, but all of the probe set intensities are below 12. When I've used PLIER previously with the same data set(with Affy's free ArrayAssist Lite program), values are much higher. I'm assuming there is some kind of a log function happening in the R version. Is there any way to turn the log function off? I've looked through the options but can't find anything that seems to make this happen. We're presently using R to compare some data with a collaborator who is using ArrayAssist. Thanks, Tarun Nayar Genome Sciences Centre Vancouver, BC [[alternative HTML version deleted]]

You can simply convert to natural scale yourself. exprs(eset) <- 2^exprs(eset) HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Tarun Nayar" <tnayar@bcgsc.ca> 05/27/05 5:29 PM >>> Hi, I've been trying to use PLIER to pre-process microarray data from 5 Rat 230A chips. After using the justPlier function, I get an exprSet, but all of the probe set intensities are below 12. When I've used PLIER previously with the same data set(with Affy's free ArrayAssist Lite program), values are much higher. I'm assuming there is some kind of a log function happening in the R version. Is there any way to turn the log function off? I've looked through the options but can't find anything that seems to make this happen. We're presently using R to compare some data with a collaborator who is using ArrayAssist. Thanks, Tarun Nayar Genome Sciences Centre Vancouver, BC [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.