Hi, We are working with affymetrix HuGene2.0 ST arrays and are trying to read in our CEL files with the oligo package. However, we are having trouble integrating our phenodata to the expression data. Please see our code and error message below. The covdesc.txt is the file with our phenodata. code: pd <-read.AnnotatedDataFrame("covdesc.txt",header=TRUE,row.name="Filen ame",sep="\t") OligoRaw<-read.celfiles(filenames=list.celfiles(), phenoData=pd, verbose = TRUE) >pData(pd) Filename Treatment Transfection 1 ACsiNS.CEL control ns_siRNA 2 ACSsi03.CEL control siRNA03 3 ANCSsi03.CEL Treated siRNA03 4 ANCSsiNS_2.CEL Treated ns_siRNA 5 DCsi03.CEL control ns_siRNA 6 DCsiNS.CEL control siRNA03 7 DNCSsi03.CEL Treated siRNA03 8 DNCSsiNS.CEL Treated ns_siRNA 9 ECsi03.CEL control ns_siRNA 10 ECsiNS.CEL control siRNA03 11 ENCSsi03.CEL Treated siRNA03 12 ENCSsiNS.CEL Treated ns_siRNA Error: > OligoRaw<-read.celfiles(filenames=list.celfiles(), phenoData=pd1, verbose = TRUE) Platform design info loaded. Reading in : ACsiNS.CEL Reading in : ACSsi03.CEL Reading in : ANCSsi03.CEL Reading in : ANCSsiNS_2.CEL Reading in : DCsi03.CEL Reading in : DCsiNS.CEL Reading in : DNCSsi03.CEL Reading in : DNCSsiNS.CEL Reading in : ECsi03.CEL Reading in : ECsiNS.CEL Reading in : ENCSsi03.CEL Reading in : ENCSsiNS.CEL Error in validObject(out) : invalid class ???GeneFeatureSet??? object: 'NChannelSet' varMetadata must have a 'channel' column Any suggestions will be appreciated! Thanks! -- output of sessionInfo(): > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] pd.hugene.2.0.st_3.8.0 RSQLite_0.11.4 DBI_0.2-7 [4] oligo_1.24.1 oligoClasses_1.22.0 affyPLM_1.36.0 [7] preprocessCore_1.22.0 arrayQualityMetrics_3.16.0 affyQCReport_1.38.0 [10] lattice_0.20-15 simpleaffy_2.36.1 gcrma_2.32.0 [13] genefilter_1.42.0 affy_1.38.1 Biobase_2.20.1 [16] BiocGenerics_0.6.0 BiocInstaller_1.10.2 loaded via a namespace (and not attached): [1] affxparser_1.32.3 affyio_1.28.0 annotate_1.38.0 AnnotationDbi_1.22.6 [5] beadarray_2.10.0 BeadDataPackR_1.12.0 Biostrings_2.28.0 bit_1.1-10 [9] Cairo_1.5-2 cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 [13] ff_2.2-11 foreach_1.4.1 GenomicRanges_1.12.4 grid_3.0.0 [17] Hmisc_3.12-2 hwriter_1.3 IRanges_1.18.2 iterators_1.0.6 [21] KernSmooth_2.23-10 latticeExtra_0.6-24 limma_3.16.6 plyr_1.8 [25] RColorBrewer_1.0-5 reshape2_1.2.2 rpart_4.1-1 setRNG_2011.11-2 [29] splines_3.0.0 stats4_3.0.0 stringr_0.6.2 survival_2.37-4 [33] SVGAnnotation_0.93-1 tools_3.0.0 vsn_3.28.0 XML_3.95-0.2 [37] xtable_1.7-1 zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.

On 7/24/2013 4:40 PM, Guest [guest] wrote: > Hi, > > We are working with affymetrix HuGene2.0 ST arrays and are trying to read in our CEL files with the oligo package. However, we are having trouble integrating our phenodata to the expression data. Please see our code and error message below. The covdesc.txt is the file with our phenodata. > > code: > > pd<-read.AnnotatedDataFrame("covdesc.txt",header=TRUE,row.name="File name",sep="\t") > > OligoRaw<-read.celfiles(filenames=list.celfiles(), phenoData=pd, verbose = TRUE) > >> pData(pd) > Filename Treatment Transfection > 1 ACsiNS.CEL control ns_siRNA > 2 ACSsi03.CEL control siRNA03 > 3 ANCSsi03.CEL Treated siRNA03 > 4 ANCSsiNS_2.CEL Treated ns_siRNA > 5 DCsi03.CEL control ns_siRNA > 6 DCsiNS.CEL control siRNA03 > 7 DNCSsi03.CEL Treated siRNA03 > 8 DNCSsiNS.CEL Treated ns_siRNA > 9 ECsi03.CEL control ns_siRNA > 10 ECsiNS.CEL control siRNA03 > 11 ENCSsi03.CEL Treated siRNA03 > 12 ENCSsiNS.CEL Treated ns_siRNA > > Error: >> OligoRaw<-read.celfiles(filenames=list.celfiles(), phenoData=pd1, verbose = TRUE) > Platform design info loaded. > Reading in : ACsiNS.CEL > Reading in : ACSsi03.CEL > Reading in : ANCSsi03.CEL > Reading in : ANCSsiNS_2.CEL > Reading in : DCsi03.CEL > Reading in : DCsiNS.CEL > Reading in : DNCSsi03.CEL > Reading in : DNCSsiNS.CEL > Reading in : ECsi03.CEL > Reading in : ECsiNS.CEL > Reading in : ENCSsi03.CEL > Reading in : ENCSsiNS.CEL > Error in validObject(out) : invalid class ???GeneFeatureSet??? object: > 'NChannelSet' varMetadata must have a 'channel' column > > Any suggestions will be appreciated! There is a varMetadata slot to the AnnotatedDataFrame, and oligo expects that there will be a column called 'channel'. A really cheap way to fix this would be to do something like x <- varMetadata(pd) x <- data.frame(x, channel = "_ALL_") varMetadata(pd) <- x and then proceed with read.celfiles(). Best, Jim > Thanks! > > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.0.0 (2013-04-03) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] pd.hugene.2.0.st_3.8.0 RSQLite_0.11.4 DBI_0.2-7 > [4] oligo_1.24.1 oligoClasses_1.22.0 affyPLM_1.36.0 > [7] preprocessCore_1.22.0 arrayQualityMetrics_3.16.0 affyQCReport_1.38.0 > [10] lattice_0.20-15 simpleaffy_2.36.1 gcrma_2.32.0 > [13] genefilter_1.42.0 affy_1.38.1 Biobase_2.20.1 > [16] BiocGenerics_0.6.0 BiocInstaller_1.10.2 > > loaded via a namespace (and not attached): > [1] affxparser_1.32.3 affyio_1.28.0 annotate_1.38.0 AnnotationDbi_1.22.6 > [5] beadarray_2.10.0 BeadDataPackR_1.12.0 Biostrings_2.28.0 bit_1.1-10 > [9] Cairo_1.5-2 cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 > [13] ff_2.2-11 foreach_1.4.1 GenomicRanges_1.12.4 grid_3.0.0 > [17] Hmisc_3.12-2 hwriter_1.3 IRanges_1.18.2 iterators_1.0.6 > [21] KernSmooth_2.23-10 latticeExtra_0.6-24 limma_3.16.6 plyr_1.8 > [25] RColorBrewer_1.0-5 reshape2_1.2.2 rpart_4.1-1 setRNG_2011.11-2 > [29] splines_3.0.0 stats4_3.0.0 stringr_0.6.2 survival_2.37-4 > [33] SVGAnnotation_0.93-1 tools_3.0.0 vsn_3.28.0 XML_3.95-0.2 > [37] xtable_1.7-1 zlibbioc_1.6.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

You have to create the AnnotatedDataFrame first. pd<-read.AnnotatedDataFrame("covdesc.txt",header=TRUE,row.name="Filena me" ,sep="\t") x <- varMetadata(pd) Best, Jim On 7/24/2013 5:03 PM, Jia, Li (NIH/NCI) [C] wrote: > Hi Jim, > > Thanks for the prompt reply. When I tested on the first command you sent > to us, it generated an error. > >> x<- varMetadata(pd) > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ?varMetadata? for > signature ?"data.frame"? > > > > Please advise again. Thanks a lot. > > Li > > On 7/24/13 4:58 PM, "James W. MacDonald"<jmacdon at="" uw.edu=""> wrote: > >> >> On 7/24/2013 4:40 PM, Guest [guest] wrote: >>> Hi, >>> >>> We are working with affymetrix HuGene2.0 ST arrays and are trying to >>> read in our CEL files with the oligo package. However, we are having >>> trouble integrating our phenodata to the expression data. Please see our >>> code and error message below. The covdesc.txt is the file with our >>> phenodata. >>> >>> code: >>> >>> >>> pd<-read.AnnotatedDataFrame("covdesc.txt",header=TRUE,row.name="Fi lename" >>> ,sep="\t") >>> >>> OligoRaw<-read.celfiles(filenames=list.celfiles(), phenoData=pd, >>> verbose = TRUE) >>> >>>> pData(pd) >>> Filename Treatment Transfection >>> 1 ACsiNS.CEL control ns_siRNA >>> 2 ACSsi03.CEL control siRNA03 >>> 3 ANCSsi03.CEL Treated siRNA03 >>> 4 ANCSsiNS_2.CEL Treated ns_siRNA >>> 5 DCsi03.CEL control ns_siRNA >>> 6 DCsiNS.CEL control siRNA03 >>> 7 DNCSsi03.CEL Treated siRNA03 >>> 8 DNCSsiNS.CEL Treated ns_siRNA >>> 9 ECsi03.CEL control ns_siRNA >>> 10 ECsiNS.CEL control siRNA03 >>> 11 ENCSsi03.CEL Treated siRNA03 >>> 12 ENCSsiNS.CEL Treated ns_siRNA >>> >>> Error: >>>> OligoRaw<-read.celfiles(filenames=list.celfiles(), phenoData=pd1, >>>> verbose = TRUE) >>> Platform design info loaded. >>> Reading in : ACsiNS.CEL >>> Reading in : ACSsi03.CEL >>> Reading in : ANCSsi03.CEL >>> Reading in : ANCSsiNS_2.CEL >>> Reading in : DCsi03.CEL >>> Reading in : DCsiNS.CEL >>> Reading in : DNCSsi03.CEL >>> Reading in : DNCSsiNS.CEL >>> Reading in : ECsi03.CEL >>> Reading in : ECsiNS.CEL >>> Reading in : ENCSsi03.CEL >>> Reading in : ENCSsiNS.CEL >>> Error in validObject(out) : invalid class ???GeneFeatureSet??? object: >>> 'NChannelSet' varMetadata must have a 'channel' column >>> >>> Any suggestions will be appreciated! >> There is a varMetadata slot to the AnnotatedDataFrame, and oligo expects >> that there will be a column called 'channel'. A really cheap way to fix >> this would be to do something like >> >> x<- varMetadata(pd) >> x<- data.frame(x, channel = "_ALL_") >> varMetadata(pd)<- x >> >> and then proceed with read.celfiles(). >> >> Best, >> >> Jim >> >> >>> Thanks! >>> >>> >>> -- output of sessionInfo(): >>> >>>> sessionInfo() >>> R version 3.0.0 (2013-04-03) >>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets methods >>> base >>> >>> other attached packages: >>> [1] pd.hugene.2.0.st_3.8.0 RSQLite_0.11.4 DBI_0.2-7 >>> [4] oligo_1.24.1 oligoClasses_1.22.0 >>> affyPLM_1.36.0 >>> [7] preprocessCore_1.22.0 arrayQualityMetrics_3.16.0 >>> affyQCReport_1.38.0 >>> [10] lattice_0.20-15 simpleaffy_2.36.1 gcrma_2.32.0 >>> [13] genefilter_1.42.0 affy_1.38.1 >>> Biobase_2.20.1 >>> [16] BiocGenerics_0.6.0 BiocInstaller_1.10.2 >>> >>> loaded via a namespace (and not attached): >>> [1] affxparser_1.32.3 affyio_1.28.0 annotate_1.38.0 >>> AnnotationDbi_1.22.6 >>> [5] beadarray_2.10.0 BeadDataPackR_1.12.0 Biostrings_2.28.0 >>> bit_1.1-10 >>> [9] Cairo_1.5-2 cluster_1.14.4 codetools_0.2-8 >>> colorspace_1.2-2 >>> [13] ff_2.2-11 foreach_1.4.1 GenomicRanges_1.12.4 >>> grid_3.0.0 >>> [17] Hmisc_3.12-2 hwriter_1.3 IRanges_1.18.2 >>> iterators_1.0.6 >>> [21] KernSmooth_2.23-10 latticeExtra_0.6-24 limma_3.16.6 >>> plyr_1.8 >>> [25] RColorBrewer_1.0-5 reshape2_1.2.2 rpart_4.1-1 >>> setRNG_2011.11-2 >>> [29] splines_3.0.0 stats4_3.0.0 stringr_0.6.2 >>> survival_2.37-4 >>> [33] SVGAnnotation_0.93-1 tools_3.0.0 vsn_3.28.0 >>> XML_3.95-0.2 >>> [37] xtable_1.7-1 zlibbioc_1.6.0 >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> 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 >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099