If you can guarantee that the order of samples in your txt file is the same as in your 'celfiles' variables, you should be okay with: pd <- read.table("phenodata.txt"**) pd <- as(pd, "AnnotatedDataFrame") TFdata <- read.celfiles(**celfiles) sampleNames(pd) <- sampleNames(TFdata) phenoData(pd) <- pd b On 6 December 2012 19:13, James W. MacDonald <jmacdon@uw.edu> wrote: > > > On 12/6/2012 1:59 PM, Bruno [guest] wrote: > >> ok sorry ill copy and past all the steps i've done after loading the >> "oligo" package. >> Thanks a lot >> >> celfiles<-list.celfiles() >> >>> celfiles >>> >> [1] "Titan_0026_838M_Freeman_838M_**A1_A05.CEL" >> "Titan_0026_838M_Freeman_838M_**A1_E09.CEL" >> "Titan_0026_838M_Freeman_838M_**A10_B07.CEL" >> [4] "Titan_0026_838M_Freeman_838M_**A2_B05.CEL" >> "Titan_0026_838M_Freeman_838M_**A3_C05.CEL" >> "Titan_0026_838M_Freeman_838M_**A3_F09.CEL" >> [7] "Titan_0026_838M_Freeman_838M_**A4_D05.CEL" >> "Titan_0026_838M_Freeman_838M_**A5_E05.CEL" >> "Titan_0026_838M_Freeman_838M_**A6_F05.CEL" >> [10] "Titan_0026_838M_Freeman_838M_**A7_G05.CEL" >> "Titan_0026_838M_Freeman_838M_**A8_H05.CEL" >> "Titan_0026_838M_Freeman_838M_**A9_A07.CEL" >> [13] "Titan_0026_838M_Freeman_838M_**B1_C07.CEL" >> "Titan_0026_838M_Freeman_838M_**B1_G09.CEL" >> "Titan_0026_838M_Freeman_838M_**B10_D09.CEL" >> [16] "Titan_0026_838M_Freeman_838M_**B2_D07.CEL" >> "Titan_0026_838M_Freeman_838M_**B3_E07.CEL" >> "Titan_0026_838M_Freeman_838M_**B4_F07.CEL" >> [19] "Titan_0026_838M_Freeman_838M_**B4_H09.CEL" >> "Titan_0026_838M_Freeman_838M_**B5_G07.CEL" >> "Titan_0026_838M_Freeman_838M_**B6_H07.CEL" >> [22] "Titan_0026_838M_Freeman_838M_**B7_A09.CEL" >> "Titan_0026_838M_Freeman_838M_**B8_B09.CEL" >> "Titan_0026_838M_Freeman_838M_**B9_C09.CEL" >> >>> pd<-read.table("phenodata.txt"**) >>> pd<-as(pd, "AnnotatedDataFrame") >>> TFdata<-read.celfiles(**celfiles, phenoData=pd) >>> >> Platform design info loaded. >> Reading in : Titan_0026_838M_Freeman_838M_**A1_A05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A1_E09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A10_B07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A2_B05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A3_C05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A3_F09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A4_D05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A5_E05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A6_F05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A7_G05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A8_H05.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**A9_A07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B1_C07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B1_G09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B10_D09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B2_D07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B3_E07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B4_F07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B4_H09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B5_G07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B6_H07.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B7_A09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B8_B09.CEL >> Reading in : Titan_0026_838M_Freeman_838M_**B9_C09.CEL >> >> Error in validObject(out) : >> invalid class “GeneFeatureSet†object: 1: sampleNames differ >> between assayData and phenoData >> invalid class “GeneFeatureSet†object: 2: sampleNames differ between >> phenoData and protocolData >> > > OK, this is a bit better, although it is still a mystery what is in your > phenoData. However, the error messages say what the problem is - the > phenoData object that you are trying to put in your GeneFeatureSet is > incompatible. > > Now I am no expert on the intricacies of the phenoData slot, because I > actually never use it. So unless you are planning on doing things with the > phenoData slot, you can just go forward without specifying it directly: > > TFdata<-read.celfiles(**celfiles) ## side note - spaces are good > > > However, it isn't difficult to see what is expected. We can just open up > an existing ExpressionSet (which GeneFeatureSet is a subset of), and see > what is in there: > > > library(affydata) > > data(Dilution) > > pData(phenoData(Dilution)) > liver sn19 scanner > 20A 20 0 1 > 20B 20 0 2 > 10A 10 0 1 > 10B 10 0 2 > > sampleNames(Dilution) > [1] "20A" "20B" "10A" "10B" > > So there are four samples here, and the row names of the phenoData match > those sample names. So the first step for you is to ensure that the row > names of the data.frame you are using to create the phenoData are identical > to the sampleNames that will result (e.g., they should be identical to your > celfiles variable). > > Best, > > Jim > > > >> -- output of sessionInfo(): >> >> >> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United >> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C >> >> [5] LC_TIME=English_United Kingdom.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] pd.hugene.1.1.st.v1_3.8.0 RSQLite_0.11.2 DBI_0.2-5 >> oligo_1.22.0 Biobase_2.18.0 >> oligoClasses_1.20.0 >> [7] BiocGenerics_0.4.0 BiocInstaller_1.8.3 >> >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.30.0 affyio_1.26.0 Biostrings_2.26.2 >> bit_1.1-9 codetools_0.2-8 ff_2.2-10 >> foreach_1.4.0 >> [8] GenomicRanges_1.10.5 IRanges_1.16.4 iterators_1.0.6 >> parallel_2.15.1 preprocessCore_1.20.0 splines_2.15.1 >> stats4_2.15.1 >> [15] tools_2.15.1 zlibbioc_1.4.0 >> >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<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 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hi List, I am having a problem reading HuGene 1.0 arrays with the oligo package. library(oligo) read.celfiles(filenames=filenames) # Could not open file ~/Downloads/SSA/original/CC_Black_(HuGene-1_0-st-v1).CEL Looking inside read.celfiles, it seems that the problem may start with getCelChipType oligo:::getCelChipType(filenames[1],TRUE) Error in read.celfile.header(x) : Could not open file ~/Downloads/SSA/original/CC_Black_(HuGene-1_0-st-v1).CEL changing the useAffyio to FALSE seems to work. oligo:::getCelChipType(filenames[1],useAffyio=FALSE) [1] "HuGene-1_0-st-v1" However the useAffyio option has been removed from read.celfiles and changing read.celfiles at this point just moves the problem further down into the function. Bye Rob > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.hugene.1.0.st.v1_3.6.0 RSQLite_0.11.2 [3] DBI_0.2-5 oligo_1.20.4 [5] oligoClasses_1.18.0 loaded via a namespace (and not attached): [1] affxparser_1.28.1 affyio_1.24.0 Biobase_2.16.0 [4] BiocGenerics_0.2.0 BiocInstaller_1.4.9 Biostrings_2.24.1 [7] bit_1.1-9 codetools_0.2-8 ff_2.2-10 [10] foreach_1.4.0 IRanges_1.14.4 iterators_1.0.6 [13] preprocessCore_1.18.0 splines_2.15.2 stats4_2.15.2 [16] tools_2.15.2 zlibbioc_1.2.0 -- Rob Dunne Fax: +61 2 9325 3200 Tel: +61 2 9325 3263 CSIRO Mathematical and Information Sciences +61 2 9325 3100 Locked Bag 17, North Ryde, New South Wales, Australia, 1670 http://www.bioinformatics.csiro.au Email: Rob.Dunne at csiro.au Java has certainly revolutionized marketing and litigation.