I think we need to update the Fusion SDK to have support for Axiom arrays. It has been on my backlog for a while. I'll bump it up. Kasper On Mon, Jul 2, 2012 at 10:13 AM, Kasper Daniel Hansen <kasperdanielhansen at="" gmail.com=""> wrote: > David, could you put up the CDF files (and hopefully also the CEL > file) somewhere where Henrik and I could have a look? > > Kasper > > On Mon, Jul 2, 2012 at 9:58 AM, David Wragg <plxdw1 at="" nottingham.ac.uk=""> wrote: >> On a related note, I've attempted to read the cdf file I've been given after managing to get the aroma.affymetrix up and running. It appears I have problems here also. >> >>> path >> [1] "annotationData/chipTypes/Axiom_GW_Gal_SNP_1.r1" >>> print(list.files(path=path)); >> [1] "Axiom_GW_Gal_SNP_1.r1.cdf" >>> cdf <- AffymetrixCdfFile$byChipType("Axiom_GW_Gal_SNP_1.r1"); >>> print(cdf); >> Error in readCdfHeader(getPathname(this)) : >> ? Failed to read the CDF file header for: annotationData/chipTypes/ Axiom_GW_Gal_SNP_1.r1/Axiom_GW_Gal_SNP_1.r1.cdf >> >> [1] "annotationData/chipTypes/Axiom_GW_Gal_SNP_1.r1/Axiom_GW_Gal_SN P_1.r1.cdf" >>> make.cdf.package(cdfFile, species="Gallus") >> Reading CDF file. >> Error in getInfoInFile(file, "CDF", unit = "Chip", property = "Name", ?: >> ? The file /home/plxdw1/HDgenotypes/annotationData/chipTypes/Axiom_ GW_Gal_SNP_1.r1/Axiom_GW_Gal_SNP_1.r1.cdf does not appear to be a CDF file. >> >> >>> 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 >> ?[3] LC_TIME=en_GB.UTF-8 ? ? ? ?LC_COLLATE=en_GB.UTF-8 >> ?[5] LC_MONETARY=en_GB.UTF-8 ? ?LC_MESSAGES=en_GB.UTF-8 >> ?[7] LC_PAPER=C ? ? ? ? ? ? ? ? LC_NAME=C >> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> ?[1] makecdfenv_1.34.0 ? ? ?BiocInstaller_1.4.7 ? ?aroma.affymetrix_2.5.0 >> ?[4] affxparser_1.28.1 ? ? ?aroma.apd_0.2.2 ? ? ? ?R.huge_0.4.0 >> ?[7] aroma.core_2.5.0 ? ? ? aroma.light_1.24.0 ? ? matrixStats_0.5.0 >> [10] R.rsp_0.7.5 ? ? ? ? ? ?R.cache_0.6.2 ? ? ? ? ?R.filesets_1.1.5 >> [13] digest_0.5.2 ? ? ? ? ? R.utils_1.12.1 ? ? ? ? R.oo_1.9.8 >> [16] R.methodsS3_1.4.2 >> >> loaded via a namespace (and not attached): >> [1] affy_1.28.0 ? ? ? ? ? affyio_1.18.0 ? ? ? ? Biobase_2.10.0 >> [4] preprocessCore_1.12.0 tcltk_2.15.1 ? ? ? ? ?tools_2.15.1 >> [7] zlibbioc_1.2.0 >> >> >> >> >> Partial output from the beginning the first line of the CDF file: >> >> C $00007bd4-6755-4d27-1aa2-004d8e005a1d Axiom_GW_Gal_1 Axiom_GW_Gal_1.r1? ? ?? ? AFFX-NP-77285336AFFX-NP-77285338AFFX-NP- 77285339AFFX-NP-77285341AFFX-NP-77285345AFFX-NP-77285346AFFX-NP- 77285348AFFX-NP-77285355AFFX-NP-77285363AFFX-NP-77285364AFFX-NP- 77285373AFFX-NP-77285376AFFX-NP-77285381AFFX-NP-77285382AFFX-NP- 77285385A >> >> >> >> >> >> Dave >> >> >> >> >> ________________________________________ >> From: Kasper Daniel Hansen [kasperdanielhansen at gmail.com] >> Sent: 02 July 2012 00:22 >> To: David Wragg >> Cc: Ben Bolstad; Henrik Bengtsson; bioconductor at r-project.org >> Subject: Re: [BioC] R 2.15.1 ReadAffy error >> >> Thanks >> >> You seem to be missing the `` (hard to see), so just try >> >> # gcc --version >> # g++ --version >> >> >> On Sun, Jul 1, 2012 at 6:50 PM, David Wragg <plxdw1 at="" nottingham.ac.uk=""> wrote: >>> *** From terminal *** >>> >>>> sessionInfo() >>> R version 2.15.1 (2012-06-22) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> locale: >>> ?[1] LC_CTYPE=en_GB.utf8 ? ? ? LC_NUMERIC=C >>> ?[3] LC_TIME=en_GB.utf8 ? ? ? ?LC_COLLATE=en_GB.utf8 >>> ?[5] LC_MONETARY=en_GB.utf8 ? ?LC_MESSAGES=en_GB.utf8 >>> ?[7] LC_PAPER=C ? ? ? ? ? ? ? ?LC_NAME=C >>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ?LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>> >>> other attached packages: >>> [1] affxparser_1.28.1 ?affyio_1.24.0 ? ? ?affy_1.34.0 ? ? ? ?Biobase_2.16.0 >>> [5] BiocGenerics_0.2.0 >>> >>> loaded via a namespace (and not attached): >>> [1] BiocInstaller_1.4.7 ? preprocessCore_1.18.0 zlibbioc_1.2.0 >>> >>> >>> >>>> setwd("~/HDgenotypes/CEL files") >>>> fns<-list.celfiles(path="~/HDgenotypes/CEL files",full.names=T) >>>> a <- read.celfile(fns[1]) >>>> b <- readCelHeader(fns[1]) >>> terminate called after throwing an instance of 'affymetrix_calvin_exceptions::DataGroupNotFoundException' >>> Aborted >>> >>> dw at dw-laptop:~$ R CMD config CC >>> gcc -std=gnu99 >>> dw at dw-laptop:~$ R CMD config CXX >>> g++ >>> dw at dw-laptop:~$ R RHOME >>> /usr/lib64/R >>> >>> dw at dw-laptop:~$ R CMD config CC --version >>> R configuration information retrieval script: 2.15.1 (r59038) >>> >>> Copyright (C) 2002-6 The R Core Team. >>> This is free software; see the GNU General Public License version 2 >>> or later for copying conditions. ?There is NO warranty. >>> dw at dw-laptop:~$ R CMD config CCC --version >>> R configuration information retrieval script: 2.15.1 (r59038) >>> >>> Copyright (C) 2002-6 The R Core Team. >>> This is free software; see the GNU General Public License version 2 >>> or later for copying conditions. ?There is NO warranty. >>> >>> >>> *** From RStudio *** >>> >>>> R.home() >>> [1] "/usr/lib64/R" >>> >>> >>> >>> >>> Regards >>> >>> Dave >>> >>> >>> ________________________________________ >>> From: Kasper Daniel Hansen [kasperdanielhansen at gmail.com] >>> Sent: 01 July 2012 17:34 >>> To: David Wragg >>> Cc: Ben Bolstad; Henrik Bengtsson; bioconductor at r-project.org >>> Subject: Re: [BioC] 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 at="" nottingham.ac.uk=""> 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 at bmbolstad.com] >>>> Sent: 01 July 2012 04:22 >>>> To: Henrik Bengtsson; DaveW [guest] >>>> Cc: plxdw1 at nottingham.ac.uk; bioconductor at r-project.org >>>> 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 at nottingham.ac.uk ; bioconductor at r-project.org >>>> 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 $.02 >>>> >>>> /Henrik >>>> (author of aroma.affymetrix) >>>> >>>> On Thu, Jun 28, 2012 at 2:16 PM, DaveW [guest] <guest at="" bioconductor.org=""> >>>> wrote: >>>>> >>>>> I'm attempting to read Affymetrix CEL files and failing miserably. Any >>>>> thoughts. >>>>> >>>>> Error in read.celfile.header(as.character(filenames[[1]])) : >>>>> ?Is /home/dw/HDgenotypes/CEL >>>>> files/Titan_0020_772G_Hannotte_772_001_D06.CEL really a CEL file? tried >>>>> reading as text, gzipped text, binary, gzipped binary, command console and >>>>> gzipped command console formats >>>>> >>>>> Here is the output of the first few lines of one of the CEL files in case >>>>> this helps anyone to spot the issue: >>>>> >>>>> dw at dw-laptop:~/HDgenotypes/CEL files$ 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 ? ? ? ? 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