[BioC] R 2.15.1 ReadAffy error

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Mon Jul 2 16:13:37 CEST 2012 

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_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 $00007bd4-6755-4d27-1aa2-004d8e005a1d Axiom_GW_Gal_1 Axiom_GW_Gal_1.r1� � ��   AFFX-NP-77285336AFFX-NP-77285338AFFX-NP-77285339AFFX-NP-77285341AFFX-NP-77285345AFFX-NP-77285346AFFX-NP-77285348AFFX-NP-77285355AFFX-NP-77285363AFFX-NP-77285364AFFX-NP-77285373AFFX-NP-77285376AFFX-NP-77285381AFFX-NP-77285382AFFX-NP-77285385A
>
>
>
>
>
> Dave
>
>
>
>
> ________________________________________
> From: Kasper Daniel Hansen [kasperdanielhansen at gmail.com]
> Sent: 02 July 2012 00:22
> To: David Wragg
> Cc: Ben Bolstad; Henrik Bengtsson; bioconductor at r-project.org
> Subject: Re: [BioC] R 2.15.1 ReadAffy error
>
> Thanks
>
> You seem to be missing the `` (hard to see), so just try
>
> # gcc --version
> # g++ --version
>
>
> On Sun, Jul 1, 2012 at 6:50 PM, David Wragg <plxdw1 at nottingham.ac.uk> wrote:
>> *** From terminal ***
>>
>>> sessionInfo()
>> R version 2.15.1 (2012-06-22)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>>  [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
>>  [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
>>  [5] LC_MONETARY=en_GB.utf8    LC_MESSAGES=en_GB.utf8
>>  [7] LC_PAPER=C                LC_NAME=C
>>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] affxparser_1.28.1  affyio_1.24.0      affy_1.34.0        Biobase_2.16.0
>> [5] BiocGenerics_0.2.0
>>
>> loaded via a namespace (and not attached):
>> [1] BiocInstaller_1.4.7   preprocessCore_1.18.0 zlibbioc_1.2.0
>>
>>
>>
>>> setwd("~/HDgenotypes/CEL files")
>>> fns<-list.celfiles(path="~/HDgenotypes/CEL files",full.names=T)
>>> a <- read.celfile(fns[1])
>>> b <- readCelHeader(fns[1])
>> terminate called after throwing an instance of 'affymetrix_calvin_exceptions::DataGroupNotFoundException'
>> Aborted
>>
>> dw at dw-laptop:~$ 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  ï¿½ text/x-calvin-integer-32
>>>> affymetrix-cel-cols  ï¿½ 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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