[BioC] R 2.15.1 ReadAffy error
David Wragg
plxdw1 at nottingham.ac.uk
Mon Jul 2 15:58:35 CEST 2012
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_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$00007bd4-6755-4d27-1aa2-004d8e005a1dAxiom_GW_Gal_1Axiom_GW_Gal_1.r1���� AFFX-NP-77285336AFFX-NP-77285338AFFX-NP-77285339AFFX-NP-77285341AFFX-NP-77285345AFFX-NP-77285346AFFX-NP-77285348AFFX-NP-77285355AFFX-NP-77285363AFFX-NP-77285364AFFX-NP-77285373AFFX-NP-77285376AFFX-NP-77285381AFFX-NP-77285382AFFX-NP-77285385A
Dave
________________________________________
From: Kasper Daniel Hansen [kasperdanielhansen at gmail.com]
Sent: 02 July 2012 00:22
To: David Wragg
Cc: Ben Bolstad; Henrik Bengtsson; bioconductor at r-project.org
Subject: Re: [BioC] R 2.15.1 ReadAffy error
Thanks
You seem to be missing the `` (hard to see), so just try
# gcc --version
# g++ --version
On Sun, Jul 1, 2012 at 6:50 PM, David Wragg <plxdw1 at nottingham.ac.uk> wrote:
> *** From terminal ***
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
> [5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] affxparser_1.28.1 affyio_1.24.0 affy_1.34.0 Biobase_2.16.0
> [5] BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
> [1] BiocInstaller_1.4.7 preprocessCore_1.18.0 zlibbioc_1.2.0
>
>
>
>> setwd("~/HDgenotypes/CEL files")
>> fns<-list.celfiles(path="~/HDgenotypes/CEL files",full.names=T)
>> a <- read.celfile(fns[1])
>> b <- readCelHeader(fns[1])
> terminate called after throwing an instance of 'affymetrix_calvin_exceptions::DataGroupNotFoundException'
> Aborted
>
> dw at dw-laptop:~$ 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.
>>>
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