I'm attempting to read Affymetrix CEL files and failing miserably. Any thoughts. Error in read.celfile.header(as.character(filenames[[1]])) : Is /home/dw/HDgenotypes/CEL files/Titan_0020_772G_Hannotte_772_001_D06.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats Here is the output of the first few lines of one of the CEL files in case this helps anyone to spot the issue: dw at dw-laptop:~/HDgenotypes/CEL files$ head Titan*H09.CEL ;
J.!affymetrix-calvin-multi- intensity60000065535-1336523928-0000026962-0000029358-0000011478en-US0 affymetrix-algorithm-nameHHT Image Calibration Cell Generation text/plain affymetrix-algorithm-version3.2.0.1515 text/plainaffymetrix-array-type???Axiom_GW_Gal_SNP_1 text/plainaffymetrix-library-package???Universal text/plainaffymetrix-cel-rows???text/x-calvin-integer-32 affymetrix-cel-cols???text/x-calvin-integer-32program-company Affymetrix, Inc. text/plain program-nameFAffymetrix Genechip Command Console text/plain program-id3.2.0.1515 text/plain)affymetrix-algorithm-param-NumPixelsToUsetext/x-calvin- integer-32+affymetrix-algorithm-param-ImageCalibratioTRUE text/plain,affymetrix-algorithm-param-FeatureExtraction -- output of sessionInfo(): > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 [4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.34.0 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 BiocInstaller_1.4.7 preprocessCore_1.18.0 tools_2.15.1 [5] zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.