The invalid class “ExpressionSet” object: sampleNames differ between phenoData and protocolData error occurs whenever the row names of the phenodata file does not match the names of the CEL files. The order of the samples in the phenoData file also matters. One way to check if they match is to pass the phenoData instance created with the AnnotatedDataFrame method to the pData function. >pData(phenodatainstance); and pass the AffyBatch object produced by a Readaffy or read.celfiles function to the sampleNames function, as shown below: > sampleNames(affydata); The number, order and string values returned by both statements should match. Manuel X. Duval, PhD University of New Haven Biology Adjunct Biological Sciences mduval@newhaven.edu Cell: 860-287-3570 [[alternative HTML version deleted]]

Dear Manuel, could you please provide a reproducible example just so I can appropriately address the issue (as needed) in the package? Thank you very much, benilton 2013/6/11 Duval, Manuel <mduval at="" newhaven.edu="">: > The invalid class ?ExpressionSet? object: sampleNames differ between phenoData and protocolData error occurs whenever the row names of the phenodata file does not match the names of the CEL files. The order of the samples in the phenoData file also matters. > > One way to check if they match is to pass the phenoData instance created with the AnnotatedDataFrame method to the pData function. >>pData(phenodatainstance); > > and pass the AffyBatch object produced by a Readaffy or read.celfiles function to the sampleNames function, as shown below: > >> sampleNames(affydata); > > The number, order and string values returned by both statements should match. > > > Manuel X. Duval, PhD > University of New Haven > Biology Adjunct > Biological Sciences > mduval at newhaven.edu > Cell: 860-287-3570 > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor