[BioC] Cel processing question

[Henrik Bengtsson]

On Fri, Jun 20, 2008 at 8:06 AM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> Hi Iain,
>
> IAIN GALLAGHER wrote:
>>
>> Hello list.
>>
>> This is not technically a bioconductor problem but... I have been
>> informed that during the last year or so Affymetrix have changed the
>> way they make / generate .CEL files. I was wondering whether this is
>> likely to affect the results one would obtain running an analysis
>> from .CEL files onwards.
>
> If you mean the change from ASCII to binary format, this happened a few
> years ago. There are some facilities to change between the formats, but this
> should be unnecessary, as most tools that you are likely to use will use
> either format without complaint.

Affymetrix has introduced a more generic binary file format (think XML
but an inhouse format) that applies to several of their file formats,
e.g. CEL and CDF.  That might be what you are thinking of.  The
affxparser package handles those files automatically because it
utilizes Affymetrix' Fusion SDK library to read the files.  So, any
package reading files using affxparser can deal with those as well.

Cheers

Henrik

>
> Best,
>
> Jim
>
>
>>
>> Thanks
>>
>> Iain
>>
>> [[alternative HTML version deleted]]
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
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