An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070524/ 8515da0d/attachment.pl

Hi Diego -- The following might help... "diego arcelli" <diego.arcelli at="" gmail.com=""> writes: > Hi to all > > I'd like to resolve this question: > > > in R 2.4 and bioconductor 1.9 I used the follow string to read my phenodata > in txt file (mysamplehe): > where "esetmysamples" is my dataset > > # Reading and setting phenodata > >> pd <- read.phenoData(filename="mysamplesphe.txt", sep="\t", header=TRUE) >> pData(esetmysamples) > > and this to remove AFFX-id probes > > ### Removing AFFX-id probes > >>ids <- (geneNames(esetmysamples)) >>ids.affx <- grep("^AFFX", ids) >>ids.noaffx <- setdiff(c(1:length(ids)), ids.affx) >>esetmysamples <- esetmysamples[ids.noaffx,] > > now, in R 2.5 and bioconductor 2.0 I must use read.'AnnotatedDataFrame' > instead of 'read.phenoData' and 'featureNames' instead of > > and here I have the Warning message: > > >> setwd(workdir) >> esetmysamples <- rma(mysamples) > Background correcting > Normalizing > Calculating Expression >> sampleNames(esetmysamples) <- smpls >> >> # Removing AFFX-id probes >> ids <- (geneNames(esetmysamples)) > Warning message: > 'geneNames' is deprecated. > Use 'featureNames' instead. > See help("Deprecated") ids <- featureNames(esetmysamples) >> ids.affx <- grep("^AFFX", ids) >> ids.noaffx <- setdiff(c(1:length(ids)), ids.affx) >> esetmysamples <- esetmysamples[ids.noaffx,] >> setwd(workdir) >> pd <- read.phenoData(filename="mysamplesphe.txt", sep="\t", header=TRUE) > Warning messages: > 1: read.phenoData is deprecated, use read.AnnotatedDataFrame instead > 2: The phenoData class is deprecated, use AnnotatedDataFrame (with > ExpressionSet) instead adf <- read.AnnotatedDataFrame(filename="mysamplesphe.txt", sep="\t", header=TRUE) The help page ?read.AnnotatedDataFrame might be helpful here. >> #esetmysamples <- new("exprSet", exprs = exprs(esetmysamples), phenoData = > pd) >> phenoData(esetmysamples) <- pd > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "phenoData<-", for > signature "ExpressionSet", "phenoData" >> phenoData(esetmysamples) <- adf Alternatively, to live with the warning but not the error, phenoData(esetmysamples) <- as(pd, "AnnotatedDataFrame") Finally, take a look at section 4 of the vignette Biobase - An introduction to Biobase and ExpressionSets for an approach that doesn't use read.AnnotatedDataFrame. Hope that helps, Martin > Can anyone help me to write the right the R.script? > > > thanks a lot > > ardi > > [[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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org