Hello, I want to use expresso for preprocessing the hgu133a-spikein data from affycompII. But there is an error: > library(affy) > path <- "z:/Microarray/hgu133a-spikein/rawdata" > celFile <- list.celfiles(path=path,full.names=TRUE); > affyBatch <- ReadAffy(filenames=celFile[1:6]); > eset1 <- expresso(affyBatch,bgcorrect.method="rma",normalize.method="quantiles" ,summary.method="medianpolish") background correction: rma normalization: quantiles PM/MM correction : expression values: medianpolish background correcting...done. normalizing...done. Fehler in function (classes, fdef, mtable) : unable to find an inherited method for function "computeExprSet", for signature "AffyBatch", "NULL", "character" ALL packages are up to date, first of all I did a update: ## *new* R session, no saved data loaded > source("http://bioconductor.org/biocLite.R") > biocLite("Biobase") > library("Biobase") > update.packages(repos=biocReposList()) > sessionInfo() 2.5.1 (2007-06-27) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETAR Y=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: hgu133atagcdf affy affyio Biobase "1.16.0" "1.14.2" "1.4.1" "1.14.1" Whats wrong? The function "computeExprSet" exists in library(affy) Thanks Markus -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de

Hi Markus -- Try providing an argument for pmcorrect.method, as in example(expresso). My hint toward this was > showMethods("computeExprSet") Function: computeExprSet (package affy) x="AffyBatch", pmcorrect.method="character", summary.method="character" This says that computeExprSet has a method defined when pmcorrect.method is of type character, whereas the error message (and glancing at the arguments of expresso) suggest that pmcorrect.method is NULL by default. Martin Markus Schmidberger <schmidb at="" ibe.med.uni-muenchen.de=""> writes: > Hello, > > I want to use expresso for preprocessing the hgu133a-spikein data from > affycompII. But there is an error: > > > library(affy) > > path <- "z:/Microarray/hgu133a-spikein/rawdata" > > celFile <- list.celfiles(path=path,full.names=TRUE); > > affyBatch <- ReadAffy(filenames=celFile[1:6]); > > eset1 <- > expresso(affyBatch,bgcorrect.method="rma",normalize.method="quantile s",summary.method="medianpolish") > > background correction: rma > normalization: quantiles > PM/MM correction : > expression values: medianpolish > background correcting...done. > normalizing...done. > Fehler in function (classes, fdef, mtable) : > unable to find an inherited method for function "computeExprSet", > for signature "AffyBatch", "NULL", "character" > > > ALL packages are up to date, first of all I did a update: > ## *new* R session, no saved data loaded >> source("http://bioconductor.org/biocLite.R") >> biocLite("Biobase") >> library("Biobase") >> update.packages(repos=biocReposList()) > > > > sessionInfo() > 2.5.1 (2007-06-27) > i386-pc-mingw32 > > locale: > LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONET ARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "utils" > "datasets" "methods" "base" > > other attached packages: > hgu133atagcdf affy affyio Biobase > "1.16.0" "1.14.2" "1.4.1" "1.14.1" > > Whats wrong? The function "computeExprSet" exists in library(affy) > > Thanks > Markus > > -- > Dipl.-Tech. Math. Markus Schmidberger > > Ludwig-Maximilians-Universit?t M?nchen > IBE - Institut f?r medizinische Informationsverarbeitung, > Biometrie und Epidemiologie > Marchioninistr. 15, D-81377 Muenchen > URL: http://ibe.web.med.uni-muenchen.de > Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org