[BioC] affxparser fails to convert AGCC format cel file

[bmb at bmbolstad.com]

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
>
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