Question: R 2.15.1 ReadAffy error
0
gravatar for Henrik Bengtsson
7.0 years ago by
United States
Henrik Bengtsson2.4k wrote:
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 ? ? ? ? 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
affyio • 1.6k views
ADD COMMENTlink modified 7.0 years ago by Ben Bolstad1.2k • written 7.0 years ago by Henrik Bengtsson2.4k
Answer: R 2.15.1 ReadAffy error
0
gravatar for Ben Bolstad
7.0 years ago by
Ben Bolstad1.2k
Ben Bolstad1.2k wrote:
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 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ 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
ADD COMMENTlink written 7.0 years ago by Ben Bolstad1.2k
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@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 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ 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 This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
ADD REPLYlink written 7.0 years ago by David Wragg40
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 ? ? ? ? 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 at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > 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 > > > This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. ? Please do not use, copy or disclose the information contained in this message or in any attachment. ?Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. > > This message has been checked for viruses but the contents of an attachment > may still contain software viruses which could damage your computer system: > you are advised to perform your own checks. Email communications with the > University of Nottingham may be monitored as permitted by UK legislation. > _______________________________________________ > 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
ADD REPLYlink written 7.0 years ago by Kasper Daniel Hansen6.4k
*** 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@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 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 at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > 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 > > > This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. > > This message has been checked for viruses but the contents of an attachment > may still contain software viruses which could damage your computer system: > you are advised to perform your own checks. Email communications with the > University of Nottingham may be monitored as permitted by UK legislation. > _______________________________________________ > 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
ADD REPLYlink written 7.0 years ago by David Wragg40
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 ? ? ? ? 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 at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> 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 >> >> >> This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. ? Please do not use, copy or disclose the information contained in this message or in any attachment. ?Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. >> >> This message has been checked for viruses but the contents of an attachment >> may still contain software viruses which could damage your computer system: >> you are advised to perform your own checks. Email communications with the >> University of Nottingham may be monitored as permitted by UK legislation. >> _______________________________________________ >> 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
ADD REPLYlink written 7.0 years ago by Kasper Daniel Hansen6.4k
dw at dw-laptop:~$ gcc --version gcc (Ubuntu 4.4.3-4ubuntu5.1) 4.4.3 Copyright (C) 2009 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. dw at dw-laptop:~$ g++ --version g++ (Ubuntu 4.4.3-4ubuntu5.1) 4.4.3 Copyright (C) 2009 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ________________________________________ From: Kasper Daniel Hansen [kasperdanielhansen@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 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 at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> 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 >> >> >> This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. >> >> This message has been checked for viruses but the contents of an attachment >> may still contain software viruses which could damage your computer system: >> you are advised to perform your own checks. Email communications with the >> University of Nottingham may be monitored as permitted by UK legislation. >> _______________________________________________ >> 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
ADD REPLYlink written 7.0 years ago by David Wragg40
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/Axi om_GW_Gal_SNP_1.r1/Axiom_GW_Gal_SNP_1.r1.cdf [1] "annotationData/chipTypes/Axiom_GW_Gal_SNP_1.r1/Axiom_GW_Gal_SNP_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$00007bd4-6755-4d27-1aa2-004d8e005a1dAxiom_GW_Gal_1Axiom_GW_Gal_1. r1???? AFFX-NP-77285336AFFX-NP-77285338AFFX-NP-77285339AFFX-NP- 77285341AFFX-NP-77285345AFFX-NP-77285346AFFX-NP-77285348AFFX-NP- 77285355AFFX-NP-77285363AFFX-NP-77285364AFFX-NP-77285373AFFX-NP- 77285376AFFX-NP-77285381AFFX-NP-77285382AFFX-NP-77285385A Dave ________________________________________ From: Kasper Daniel Hansen [kasperdanielhansen@gmail.com] Sent: 02 July 2012 00:22 To: David Wragg Cc: Ben Bolstad; Henrik Bengtsson; bioconductor at r-project.org Subject: Re: [BioC] R 2.15.1 ReadAffy error Thanks You seem to be missing the `` (hard to see), so just try # gcc --version # g++ --version On Sun, Jul 1, 2012 at 6:50 PM, David Wragg <plxdw1 at="" nottingham.ac.uk=""> wrote: > *** From terminal *** > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C > [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 > [5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affxparser_1.28.1 affyio_1.24.0 affy_1.34.0 Biobase_2.16.0 > [5] BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] BiocInstaller_1.4.7 preprocessCore_1.18.0 zlibbioc_1.2.0 > > > >> setwd("~/HDgenotypes/CEL files") >> fns<-list.celfiles(path="~/HDgenotypes/CEL files",full.names=T) >> a <- read.celfile(fns[1]) >> b <- readCelHeader(fns[1]) > terminate called after throwing an instance of 'affymetrix_calvin_exceptions::DataGroupNotFoundException' > Aborted > > dw at dw-laptop:~$ 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 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 at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> 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 >> >> >> This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. >> >> This message has been checked for viruses but the contents of an attachment >> may still contain software viruses which could damage your computer system: >> you are advised to perform your own checks. Email communications with the >> University of Nottingham may be monitored as permitted by UK legislation. >> _______________________________________________ >> 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
ADD REPLYlink written 7.0 years ago by David Wragg40
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/A xiom_GW_Gal_SNP_1.r1/Axiom_GW_Gal_SNP_1.r1.cdf > > [1] "annotationData/chipTypes/Axiom_GW_Gal_SNP_1.r1/Axiom_GW_Gal_SNP _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_G W_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 ? ? ? ? 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 at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> _______________________________________________ >>> 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 >>> >>> >>> This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. ? Please do not use, copy or disclose the information contained in this message or in any attachment. ?Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. >>> >>> This message has been checked for viruses but the contents of an attachment >>> may still contain software viruses which could damage your computer system: >>> you are advised to perform your own checks. Email communications with the >>> University of Nottingham may be monitored as permitted by UK legislation. >>> _______________________________________________ >>> 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
ADD REPLYlink written 7.0 years ago by Kasper Daniel Hansen6.4k
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 ? ? ? ? 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 at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>>> This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. ? Please do not use, copy or disclose the information contained in this message or in any attachment. ?Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. >>>> >>>> This message has been checked for viruses but the contents of an attachment >>>> may still contain software viruses which could damage your computer system: >>>> you are advised to perform your own checks. Email communications with the >>>> University of Nottingham may be monitored as permitted by UK legislation. >>>> _______________________________________________ >>>> 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
ADD REPLYlink written 7.0 years ago by Kasper Daniel Hansen6.4k
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