Open source for bioinformatics ()

DaveW [guest] | 28 Jun 2012 23:16

R 2.15.1 ReadAffy error


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-US0affymetrix-algorithm-nameHHT
Image Calibration Cell
Generation
text/plainaffymetrix-algorithm-version3.2.0.1515
text/plainaffymetrix-array-typeï¿½Axiom_GW_Gal_SNP_1
text/plainaffymetrix-library-packageï¿½Universal
text/plainaffymetrix-cel-rowsï¿½text/x-calvin-integer-32affymetrix-cel-colsï¿½text/x-calvin-integer-32program-company
Affymetrix, Inc.
text/plain
          program-nameFAffymetrix Genechip Command Console
text/plain
program-id3.2.0.1515
text/plain)affymetrix-algorithm-param-NumPixelsToUsetext/x-calvin-integer-32+affymetrix-algorithm-param-ImageCalibratioTRUE
text/plain,affymetrix-algorithm-param-FeatureExtraction

 -- output of sessionInfo(): 

> sessionInfo()

(Continue reading)

Henrik Bengtsson | 1 Jul 2012 02:45

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Re: R 2.15.1 ReadAffy error

Looks like it is a CEL file in the "new" Calvin CEL file format.  Not
sure whether affyio::read.celfile.header() supports this or not.
affxparser::readCelHeader() should - try that first to verify that you
got valid CEL files.  If that is the case, and affyio doesn't support
Calvin CEL files, then you can use affxparser::convertCel() to convert
them to good old XDA/binary CEL files, which affyio certainly
supports.

FYI, other Affymetrix-related packages handle Calvin CEL files
directly (particularly those utilizing affxparser), including
aroma.affymetrix.

My $.02

/Henrik
(author of aroma.affymetrix)

On Thu, Jun 28, 2012 at 2:16 PM, DaveW [guest] <guest@...> wrote:
>
> I'm attempting to read Affymetrix CEL files and failing miserably. Any thoughts.
>
> Error in read.celfile.header(as.character(filenames[[1]])) :
>  Is /home/dw/HDgenotypes/CEL files/Titan_0020_772G_Hannotte_772_001_D06.CEL really a CEL file?
tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command
console formats
>
> Here is the output of the first few lines of one of the CEL files in case this helps anyone to spot the issue:
>
> dw <at> dw-laptop:~/HDgenotypes/CEL files$ head Titan*H09.CEL
> ;

(Continue reading)

Ben Bolstad | 1 Jul 2012 05:22

Re: R 2.15.1 ReadAffy error

Multichannel Calvin CEL files can be read using

affyio::read.celfile()

Based on the sessionInfo() I'm guessing the OP is trying to use ReadAffy() 
from the affy package which would not be appropriate for a SNP array. 
However, I don't recall at the current time whether I ever fixed 
affyio::read.celfile.header() for such files.

Best,

Ben

-----Original Message----- 
From: Henrik Bengtsson
Sent: Saturday, June 30, 2012 5:45 PM
To: DaveW [guest]
Cc: plxdw1@... ; bioconductor@...
Subject: Re: [BioC] R 2.15.1 ReadAffy error

Looks like it is a CEL file in the "new" Calvin CEL file format.  Not
sure whether affyio::read.celfile.header() supports this or not.
affxparser::readCelHeader() should - try that first to verify that you
got valid CEL files.  If that is the case, and affyio doesn't support
Calvin CEL files, then you can use affxparser::convertCel() to convert
them to good old XDA/binary CEL files, which affyio certainly
supports.

FYI, other Affymetrix-related packages handle Calvin CEL files
directly (particularly those utilizing affxparser), including

(Continue reading)

David Wragg | 1 Jul 2012 13:13

Picon

Picon

Re: R 2.15.1 ReadAffy error

Thanks guys

affyio::read.celfile() appears to have worked

The affyxparser suggestion caused Rstudio to crash, I haven't tried it from the terminal to see if it's an
Rstudio issue. As the affyio suggestion worked I didn't pursue the other suggestion with affyxparser.
The aroma.affymetrix package requires dependency aroma.light which is not available for R 2.15.1.

Regards

Dave

________________________________________
From: Ben Bolstad [bmb@...]
Sent: 01 July 2012 04:22
To: Henrik Bengtsson; DaveW [guest]
Cc: plxdw1@...; bioconductor@...
Subject: Re: [BioC] R 2.15.1 ReadAffy error

Multichannel Calvin CEL files can be read using

affyio::read.celfile()

Based on the sessionInfo() I'm guessing the OP is trying to use ReadAffy()
from the affy package which would not be appropriate for a SNP array.
However, I don't recall at the current time whether I ever fixed
affyio::read.celfile.header() for such files.

Best,

(Continue reading)

Kasper Daniel Hansen | 1 Jul 2012 18:34

Picon

Re: R 2.15.1 ReadAffy error

I am surprised aroma.light is not available.

Anyway, I am interested in the affxparser crash.  (Just to confirm,
the same file parses fine with affyio?).  Could you tell me the
following
1) The version of affxparser (not listed in your sessionInfo() above)
2) The output (from a command prompt) of (remove # that indicates the
command prompt)
# R CMD config CC
# R CMD config CXX
# R RHOME
3) the output (from a command prompt) of
# `R CMD config CC` --version
# `R CMD config CXX` --version
4) The output from within R studio of
> R.home()

Best,
Kasper

On Sun, Jul 1, 2012 at 7:13 AM, David Wragg <plxdw1@...> wrote:
> Thanks guys
>
> affyio::read.celfile() appears to have worked
>
> The affyxparser suggestion caused Rstudio to crash, I haven't tried it from the terminal to see if it's an
Rstudio issue. As the affyio suggestion worked I didn't pursue the other suggestion with affyxparser.
The aroma.affymetrix package requires dependency aroma.light which is not available for R 2.15.1.
>
> Regards

(Continue reading)

David Wragg | 2 Jul 2012 00:50

Picon

Picon

Re: R 2.15.1 ReadAffy error

*** 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

(Continue reading)

Kasper Daniel Hansen | 2 Jul 2012 01:22

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Re: 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@...> 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):

(Continue reading)

David Wragg | 2 Jul 2012 01:25

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Re: R 2.15.1 ReadAffy error

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@...]
Sent: 02 July 2012 00:22
To: David Wragg
Cc: Ben Bolstad; Henrik Bengtsson; bioconductor@...
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@...> wrote:
> *** From terminal ***
>
>> sessionInfo()

(Continue reading)

David Wragg | 2 Jul 2012 15:58

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Re: R 2.15.1 ReadAffy error

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

(Continue reading)

Kasper Daniel Hansen | 2 Jul 2012 16:13

Picon

Re: R 2.15.1 ReadAffy error

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)

(Continue reading)

Kasper Daniel Hansen | 2 Jul 2012 16:19

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Re: R 2.15.1 ReadAffy error

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_SNP_1.r1.cdf"
>>> make.cdf.package(cdfFile, species="Gallus")
>> Reading CDF file.
>> Error in getInfoInFile(file, "CDF", unit = "Chip", property = "Name",  :
>>   The file

(Continue reading)

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