1 Jul 2012 18:34
Re: R 2.15.1 ReadAffy error
I am surprised aroma.light is not available. Anyway, I am interested in the affxparser crash. (Just to confirm, the same file parses fine with affyio?). Could you tell me the following 1) The version of affxparser (not listed in your sessionInfo() above) 2) The output (from a command prompt) of (remove # that indicates the command prompt) # R CMD config CC # R CMD config CXX # R RHOME 3) the output (from a command prompt) of # `R CMD config CC` --version # `R CMD config CXX` --version 4) The output from within R studio of > R.home() Best, Kasper On Sun, Jul 1, 2012 at 7:13 AM, David Wragg <plxdw1@...> wrote: > Thanks guys > > affyio::read.celfile() appears to have worked > > The affyxparser suggestion caused Rstudio to crash, I haven't tried it from the terminal to see if it's an Rstudio issue. As the affyio suggestion worked I didn't pursue the other suggestion with affyxparser. The aroma.affymetrix package requires dependency aroma.light which is not available for R 2.15.1. > > Regards > > Dave > > > ________________________________________ > From: Ben Bolstad [bmb@...] > Sent: 01 July 2012 04:22 > To: Henrik Bengtsson; DaveW [guest] > Cc: plxdw1@...; bioconductor@... > Subject: Re: [BioC] R 2.15.1 ReadAffy error > > Multichannel Calvin CEL files can be read using > > affyio::read.celfile() > > Based on the sessionInfo() I'm guessing the OP is trying to use ReadAffy() > from the affy package which would not be appropriate for a SNP array. > However, I don't recall at the current time whether I ever fixed > affyio::read.celfile.header() for such files. > > Best, > > Ben > > -----Original Message----- > From: Henrik Bengtsson > Sent: Saturday, June 30, 2012 5:45 PM > To: DaveW [guest] > Cc: plxdw1@... ; bioconductor@... > Subject: Re: [BioC] R 2.15.1 ReadAffy error > > Looks like it is a CEL file in the "new" Calvin CEL file format. Not > sure whether affyio::read.celfile.header() supports this or not. > affxparser::readCelHeader() should - try that first to verify that you > got valid CEL files. If that is the case, and affyio doesn't support > Calvin CEL files, then you can use affxparser::convertCel() to convert > them to good old XDA/binary CEL files, which affyio certainly > supports. > > FYI, other Affymetrix-related packages handle Calvin CEL files > directly (particularly those utilizing affxparser), including > aroma.affymetrix. > > My $.02 > > /Henrik > (author of aroma.affymetrix) > > On Thu, Jun 28, 2012 at 2:16 PM, DaveW [guest] <guest@...> > wrote: >> >> I'm attempting to read Affymetrix CEL files and failing miserably. Any >> thoughts. >> >> Error in read.celfile.header(as.character(filenames[[1]])) : >> Is /home/dw/HDgenotypes/CEL >> files/Titan_0020_772G_Hannotte_772_001_D06.CEL really a CEL file? tried >> reading as text, gzipped text, binary, gzipped binary, command console and >> gzipped command console formats >> >> Here is the output of the first few lines of one of the CEL files in case >> this helps anyone to spot the issue: >> >> dw <at> dw-laptop:~/HDgenotypes/CEL files$ 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-version 3.2.0.1515 >> text/plain affymetrix-array-type�Axiom_GW_Gal_SNP_1 >> text/plain affymetrix-library-package�Universal >> text/plain affymetrix-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-id 3.2.0.1515 >> text/plain)affymetrix-algorithm-param-NumPixelsToUse >> text/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. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@... >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > This message and any attachment are intended solely for the addressee and may contain confidential information. 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