[BioC] affxparser fails to convert AGCC format cel file

[Henrik Bengtsson]

Hi Guido,

regarding affxparser: When writing a v4 CEL header, affxparser need
the DAT header, which is not readily available in AGCC CEL files so
affxparser will try to generate a valid one from what is available.
It seems like it fails in this case.  I cannot say more until I see
the CEL file.  Please let me (here or offline) know how I can download
this CEL file (I cannot receive attachments > 19MB).

/Henrik

On 10/10/07, Steiner, Guido <guido.steiner at roche.com> wrote:
> 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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