[BioC] affxparser fails to convert AGCC format cel file

[Steiner, Guido]

Ben,
just wanted to inform you that I sent the file to Henrik now.
G.

-----Original Message-----
From: bmb at bmbolstad.com [mailto:bmb at bmbolstad.com] 
Sent: Thursday, October 11, 2007 7:28 PM
To: Henrik Bengtsson
Cc: Steiner, Guido {PRBI~Basel}; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] affxparser fails to convert AGCC format cel file

Henrik,

I can send you the file later if you want if you can't get it from Guido
(since I have received it myself), but you have correctly surmised that
there is a problem related to the non-existence of the DatHeader in this
particular CEL file. It is not how ever true to say that the DAT header
is
not readily available in the AGCC CEL file, provision is made for
storing
it in a parental header in the file format documentation (although that
is
no guarantee that it will exist, the test files I had been using for
affyio all had it existing). But I am sure you'd know better than I how
easy that is to access via the Fusion SDK.

Interestingly enough I was able to successfully read this file just fine
with my installation using ReadAffy(). Only the affyio function
read.celfile.header() with info="full" failed in my brief testing.


Ben




> 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
>>
>> Confidentiality Note: This message is intended only for
>> ...{{dropped:12}}
>>
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>
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