Hi, I would like to suggest a change to the code for MAplot. When you call MAplot(pairs=TRUE) for Affybatch objects, double logs are taken; you can see this in the affy vignette (Oct 13, 2005) on pg 11 - the A values only range from 2 - 4. MAplot by default takes the logs, but so does mva.pairs, which is called when pairs=T. One solution is to use MAplot(abatch, pairs=T, log=F) , but it would easier if the MAplot code for Affybatch objects was changed to: if (!pairs) { lots of stuff omitted } else { if (is.null(subset)) subset <- 1:ncol(x) mva.pairs(x[, subset], log.it=FALSE...) ##add the log.it=F option } } Maybe this is what Simon Lin was having trouble with in his Nov 14, 2005 e-mail? Cheers, Jenny Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

Thank you for your clear bug report, it makes tracking and fixing things much easier. This change has been made to the development version of affy. Ben On Wed, 2005-11-30 at 17:25 -0600, Jenny Drnevich wrote: > Hi, > > I would like to suggest a change to the code for MAplot. When you call > MAplot(pairs=TRUE) for Affybatch objects, double logs are taken; you can > see this in the affy vignette (Oct 13, 2005) on pg 11 - the A values only > range from 2 - 4. MAplot by default takes the logs, but so does mva.pairs, > which is called when pairs=T. One solution is to use MAplot(abatch, > pairs=T, log=F) , but it would easier if the MAplot code for Affybatch > objects was changed to: > > if (!pairs) { lots of stuff omitted } > else { > if (is.null(subset)) > subset <- 1:ncol(x) > mva.pairs(x[, subset], log.it=FALSE...) ##add the log.it=F > option > } > } > > Maybe this is what Simon Lin was having trouble with in his Nov 14, 2005 > e-mail? > > Cheers, > Jenny > > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor