[BioC] R 2.15.1 ReadAffy error

Sun Jul 1 13:13:00 CEST 2012

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-typeï¿½Axiom_GW_Gal_SNP_1
> text/plain affymetrix-library-packageï¿½Universal
> 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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