Hi I'm trying to read in cel file names from Affy MoGene-2_0-st arrays, however I am receiving error message indicating that my cel file names are not of the character class when it appears that they are. My phenodata is read in successfully. Here is my code and error: >celfiles = list.files(path = ".", pattern = ".CEL$", all.files = FALSE, full.names = FALSE, recursive = FALSE, ignore.case = FALSE); >pd<-read.AnnotatedDataFrame("covdesc.txt",header=TRUE,row.name="Filen ame" ,sep="\t") > exp.data = read.celfiles(filenames=celfiles,phenodata=pd) Error: is.character(filenames) is not TRUE > class(celfiles) [1] "character" > is.character(celfiles) [1] TRUE Any advice will be appreciated. Thanks! -- output of sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) 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] affyPLM_1.36.0 preprocessCore_1.22.0 arrayQualityMetrics_3.16.0 [4] affyQCReport_1.38.0 lattice_0.20-15 simpleaffy_2.36.1 [7] gcrma_2.32.0 genefilter_1.42.0 affy_1.38.1 [10] pd.mogene.2.0.st_2.12.0 RSQLite_0.11.4 DBI_0.2-7 [13] oligo_1.24.2 Biobase_2.20.1 oligoClasses_1.22.0 [16] BiocGenerics_0.6.0 BiocInstaller_1.10.4 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_1.2-4 [13] ff_2.2-12 foreach_1.4.1 GenomicRanges_1.12.5 grid_3.0.1 [17] Hmisc_3.12-2 hwriter_1.3 IRanges_1.18.4 iterators_1.0.6 [21] latticeExtra_0.6-26 limma_3.16.8 plyr_1.8 RColorBrewer_1.0-5 [25] reshape2_1.2.2 rpart_4.1-1 setRNG_2011.11-2 splines_3.0.1 [29] stats4_3.0.1 stringr_0.6.2 survival_2.37-4 SVGAnnotation_0.93-1 [33] tools_3.0.1 vsn_3.28.0 XML_3.95-0.2 xtable_1.7-1 [37] zlibbioc_1.6.0 > -- Sent via the guest posting facility at bioconductor.org.

Does exp.data <- read.celfiles(list.celfiles(), phenodata=pd) work? Otherwise, please give the output from celfiles and traceback() after the error. Best, Jim On Monday, October 28, 2013 2:50:10 PM, oligo user [guest] wrote: > > Hi I'm trying to read in cel file names from Affy MoGene-2_0-st arrays, however I am receiving error message indicating that my cel file names are not of the character class when it appears that they are. My phenodata is read in successfully. > > Here is my code and error: > > >> celfiles = list.files(path = ".", pattern = ".CEL$", all.files = FALSE, > full.names = FALSE, recursive = FALSE, ignore.case = FALSE); > >> pd<-read.AnnotatedDataFrame("covdesc.txt",header=TRUE,row.name="Fil ename" ,sep="\t") > >> exp.data = read.celfiles(filenames=celfiles,phenodata=pd) > Error: is.character(filenames) is not TRUE > >> class(celfiles) > [1] "character" > >> is.character(celfiles) > [1] TRUE > > > Any advice will be appreciated. > > Thanks! > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.0.1 (2013-05-16) > 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] affyPLM_1.36.0 preprocessCore_1.22.0 arrayQualityMetrics_3.16.0 > [4] affyQCReport_1.38.0 lattice_0.20-15 simpleaffy_2.36.1 > [7] gcrma_2.32.0 genefilter_1.42.0 affy_1.38.1 > [10] pd.mogene.2.0.st_2.12.0 RSQLite_0.11.4 DBI_0.2-7 > [13] oligo_1.24.2 Biobase_2.20.1 oligoClasses_1.22.0 > [16] BiocGenerics_0.6.0 BiocInstaller_1.10.4 > > 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_1.2-4 > [13] ff_2.2-12 foreach_1.4.1 GenomicRanges_1.12.5 grid_3.0.1 > [17] Hmisc_3.12-2 hwriter_1.3 IRanges_1.18.4 iterators_1.0.6 > [21] latticeExtra_0.6-26 limma_3.16.8 plyr_1.8 RColorBrewer_1.0-5 > [25] reshape2_1.2.2 rpart_4.1-1 setRNG_2011.11-2 splines_3.0.1 > [29] stats4_3.0.1 stringr_0.6.2 survival_2.37-4 SVGAnnotation_0.93-1 > [33] tools_3.0.1 vsn_3.28.0 XML_3.95-0.2 xtable_1.7-1 > [37] 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