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Hi Peter, What's your sessionInfo()? I suspect you might need to upgrade to the latest version of the package ... Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Peter Lambert Sent: 24 February 2007 21:24 To: bioconductor at stat.math.ethz.ch Subject: [BioC] SimpleAffy - problem with pairwise.comparison(),can't construct PairComp object Hi, I've been using some of the SimpleAffy functions to analyze some GEO experiments. I have the following exprSet: > Data Expression Set (exprSet) with 22690 genes 8 samples phenoData object with 1 variables and 8 cases varLabels tissue: read from file > pData(Data) tissue GSM73331 control GSM73332 control GSM73333 control GSM73334 control GSM73335 dystrophic GSM73336 dystrophic GSM73337 dystrophic GSM73338 dystrophic > res<-pairwise.comparison(Data,"tissue",c("control","dystrophic"),logge > d=F) Error in validObject(.Object) : invalid class "PairComp" object: invalid object for slot "pData" in class "PairComp": got class "factor", should be or extend class "data.frame" The problem seems to be in the get.fold.change.and.t.test() function, where the pData object comes out as a factor for some reason, and thus the new PairComp object can't be constructed. I don't have this problem when I read in cel files and phenodata using ReadAffy, and then use rma() to construct an exprSet. For the GEO data, I'm constructing the exprSet using the following: p<-read.table(file=GSE3252_series_matrix.txt,header=T,row.names=1, comment.char="!") pheno<-read.phenoData("pdata.txt",sep="\t",header=T,row.names=1) Data<-new('exprSet',exprs=as.matrix(p),phenoData=pheno) I would appreciate any insight or help. Thanks, Peter Lambert [[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 -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}