[BioC] affxparser fails to convert AGCC format cel file

[Steiner, Guido]

Ben,
that's a very kind offer which I am delighted to accept.
Cel data will fly directly to you, and here's the sessionInfo
for the others as well.
Best,
Guido

R version 2.6.0 (2007-10-03) 
ia64-unknown-linux-gnu 

locale:
C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods

[8] base     

other attached packages:
[1] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.0        
[4] Biobase_1.16.0      

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15


-----Original Message-----
From: bmb at bmbolstad.com [mailto:bmb at bmbolstad.com] 
Sent: Wednesday, October 10, 2007 5:24 PM
To: Steiner, Guido {PRBI~Basel}
Cc: bmb at bmbolstad.com; bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] affxparser fails to convert AGCC format cel file

Could you give us your sessionInfo()?

One guess might be that your file is in someway corrupted? I would be
happy to take your cel file and have a look at it.

Best,

Ben


>
> 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
> ...{{dropped:12}}
>>
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>>
>
>