[BioC] affxparser fails to convert AGCC format cel file

[Steiner, Guido]

Ben,
ReadAffy() is (not surprisingly, maybe) the first thing I tried
to import the file. This is what happened:

*** caught segfault ***
address 0x1ffffffffffffff8, cause 'memory not mapped'

Traceback:
 1: .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra,
ref.cdfName, dim.intensity, verbose, PACKAGE = "affyio")
 2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData,
description = l$description, notes = notes, compress = compress,
rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra,
verbose = verbose, sd = sd, cdfname = cdfname)
 3: ReadAffy("17F_Liver_TXST20060258.CEL")




-----Original Message-----
From: bmb at bmbolstad.com [mailto:bmb at bmbolstad.com] 
Sent: Wednesday, October 10, 2007 3:46 PM
To: Steiner, Guido {PRBI~Basel}
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] affxparser fails to convert AGCC format cel file

I can't speak for affxparser (which I am sure has support for these
files
in some way), but the latest version of affyio (the one in the recent
BioC
2.1 release) should handle AGCC format cel files (and gzipped versions
of
the same, keeping with historical support patterns). What does this
mean?
It means if you use ReadAffy() to create your affybatch it should be
automatically handled.

Best,

Ben



> Hi,
>
> I just tried affxparser on an example CEL file from the new Affymetrix
>
> Command Console software.
>
>
>
>> library(affxparser)
>
>> convertCel("agcc.cel","gcos.cel")
>
> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument
>
>
>
>> createCel("test.cel",header=readCelHeader("agcc.cel"))
>
> Error in sprintf("DatHeader=%s\n", datHeader) : zero-length argument
>
>
>
> So the error seems to happen at the createCell stage already.
>
> Reading the cel file with readCel does work!
>
> I have R 2.6.0/BioC 2.1 and affxparser version 1.10.0.
>
> Chip type is RAT_230 (I can provide the cel file if someone is
>
> interested).
>
>
>
> Any ideas how to solve this? (As an alternative - it would be fully
>
> sufficient for me to use readCel if there was a method to get the
>
> output into an AffyBatch object.)
>
>
>
> Regards,
>
> Guido
>
>
>
>
>
> --
> Guido Steiner, PhD
> F. Hoffmann-La Roche AG
> PRBI-M Scientific Methods and Algorithms
> Building 65/318B
> CH-4070 Basel
> Tel. +41 61 688 3329
>
> Confidentiality Note: This message is intended only for
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>
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