Dear all, I would like to use affycomp for my data, but even using the example data "s_RMA.csv" I get the following error when trying to read the data: > s <- read.spikein("s_RMA.csv") Error in function (classes, fdef, mtable) : unable to find an inherited method for function "pData", for signature "phenoData" > sessionInfo() R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1 locale: C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] affycomp_1.18.0 Biobase_2.2.1 > Do you know the reason for this error? Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._

Dear Rafael Meanwhile I looked at the source code of "affycomp" and realized that it contains defunct Biobase classes. When changing the code for function "read.spikein" to: read.spikein <- function(filename,cdfName=c("hgu95a","hgu133a"), remove.xhyb=TRUE){ cdfName <- match.arg(cdfName) s <- read.csv(filename,check.names=FALSE,row.names=1) samplenames <- colnames(s) ##remove the .cel if its there samplenames <- sub("\\.gz$","",samplenames,ignore.case=TRUE) samplenames <- sub("\\.Z$","",samplenames,ignore.case=TRUE) samplenames <- sub("\\.cel$","",samplenames,ignore.case=TRUE) colnames(s) <- samplenames ##read phenodata if(cdfName=="hgu95a"){ data(spikein.phenodata) pd <- spikein.phenodata } if(cdfName=="hgu133a"){ data(hgu133a.spikein.phenodata) pd <- hgu133a.spikein.phenodata } pd <- as(pd,"AnnotatedDataFrame") #<== new ##putit in order s <- s[,rownames(pData(pd))] s <- log(s) #<== new s <- new("ExpressionSet",exprs=as.matrix(s),phenoData=pd) #delete s <- exprset.log(s) ##take log if(remove.xhyb & cdfName=="hgu133a") s <- remove.hgu133a.xhyb(s) return(s) } then I can import the example using: > s <- read.spikein.test("s_rma.csv") However, then I get the next error: > assess.rma <- assessSpikeIn(s, method.name="RMA") Performing 6 assessments that will take a few minutes.....Error: 'geneNames' is defunct. Use 'featureNames' instead. See help("Defunct") and help("Biobase-defunct"). > It would be great if you could update the "affycomp" package asap to work with BioC 2.3. Thank you in advance. Best regards Christian cstrato wrote: > Dear all, > > I would like to use affycomp for my data, but even using the example > data "s_RMA.csv" I get the following error when trying to read the data: > > > s <- read.spikein("s_RMA.csv") > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "pData", for > signature "phenoData" > > > sessionInfo() > R version 2.8.0 (2008-10-20) > i386-apple-darwin8.11.1 > > locale: > C > > attached base packages: > [1] tools stats graphics grDevices utils datasets > methods [8] base > other attached packages: > [1] affycomp_1.18.0 Biobase_2.2.1 > > > Do you know the reason for this error? > > Best regards > Christian > _._._._._._._._._._._._._._._._._._ > C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a > V.i.e.n.n.a A.u.s.t.r.i.a > e.m.a.i.l: cstrato at aon.at > _._._._._._._._._._._._._._._._._._ > > _______________________________________________ > 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 > >

Dear Benilton Thank you for this information, using affycomp_1.19.3 solved my problem. I have tested that it works with R 2.8.0, however I had to change the Depends field of DESCRIPTION to R (>=R.2.8.0), Biobase (>=2.2.1). Best regards Christian Benilton Carvalho wrote: > I'm not in position to give it a try now, but have you tried affycomp > in BioC-devel??? > > I did fix something similar to this there not long ago. > > Thank you, > > b > > On Dec 15, 2008, at 7:52 PM, cstrato wrote: > >> Dear Rafael >> >> Meanwhile I looked at the source code of "affycomp" and realized that it >> contains defunct Biobase classes. >> >> When changing the code for function "read.spikein" to: >> >> read.spikein <- function(filename,cdfName=c("hgu95a","hgu133a"), >> remove.xhyb=TRUE){ >> cdfName <- match.arg(cdfName) >> s <- read.csv(filename,check.names=FALSE,row.names=1) >> samplenames <- colnames(s) >> ##remove the .cel if its there >> samplenames <- sub("\\.gz$","",samplenames,ignore.case=TRUE) >> samplenames <- sub("\\.Z$","",samplenames,ignore.case=TRUE) >> samplenames <- sub("\\.cel$","",samplenames,ignore.case=TRUE) >> colnames(s) <- samplenames >> ##read phenodata >> if(cdfName=="hgu95a"){ >> data(spikein.phenodata) >> pd <- spikein.phenodata >> } >> if(cdfName=="hgu133a"){ >> data(hgu133a.spikein.phenodata) >> pd <- hgu133a.spikein.phenodata >> } >> pd <- as(pd,"AnnotatedDataFrame") #<== new >> ##putit in order >> s <- s[,rownames(pData(pd))] >> s <- log(s) #<== new >> s <- new("ExpressionSet",exprs=as.matrix(s),phenoData=pd) >> #delete s <- exprset.log(s) ##take log >> if(remove.xhyb & cdfName=="hgu133a") s <- remove.hgu133a.xhyb(s) >> return(s) >> } >> >> then I can import the example using: >> >>> s <- read.spikein.test("s_rma.csv") >> >> However, then I get the next error: >> >>> assess.rma <- assessSpikeIn(s, method.name="RMA") >> Performing 6 assessments that will take a few minutes.....Error: >> 'geneNames' is defunct. >> Use 'featureNames' instead. >> See help("Defunct") and help("Biobase-defunct"). >>> >> >> It would be great if you could update the "affycomp" package asap to >> work with BioC 2.3. >> >> Thank you in advance. >> Best regards >> Christian >> >> >> cstrato wrote: >>> Dear all, >>> >>> I would like to use affycomp for my data, but even using the example >>> data "s_RMA.csv" I get the following error when trying to read the >>> data: >>> >>>> s <- read.spikein("s_RMA.csv") >>> Error in function (classes, fdef, mtable) : >>> unable to find an inherited method for function "pData", for >>> signature "phenoData" >>> >>>> sessionInfo() >>> R version 2.8.0 (2008-10-20) >>> i386-apple-darwin8.11.1 >>> >>> locale: >>> C >>> >>> attached base packages: >>> [1] tools stats graphics grDevices utils datasets >>> methods [8] base >>> other attached packages: >>> [1] affycomp_1.18.0 Biobase_2.2.1 > >>> >>> Do you know the reason for this error? >>> >>> Best regards >>> Christian >>> _._._._._._._._._._._._._._._._._._ >>> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a >>> V.i.e.n.n.a A.u.s.t.r.i.a >>> e.m.a.i.l: cstrato at aon.at >>> _._._._._._._._._._._._._._._._._._ >>> >>> _______________________________________________ >>> 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 >>> >>> >> >> _______________________________________________ >> 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 >