[BioC] Working with Affymetrix Files

[Henrik Bengtsson]

Use affxparser or affyio to read the CEL files - way better than
convert binary CELs to text and then use obsolete parser to read them.

Cheers

Henrik

On Tue, Jun 24, 2008 at 8:54 AM, Matthew McCormack
<mccormack at molbio.mgh.harvard.edu> wrote:
> You might want to try *CEL File Conversion* Tool found at
> http://www.affymetrix.com/support/developer/tools/devnettools.affx.
> This is used to . ..  "convert all Affymetrix CEL files in a specified
> directory from version 3 format (ASCII - MAS 5 compatible format) _to
> and from_ version 4 format (binary - GCOS compatible format). You files
> may be version 4. If you convert them to version 3, you may have what
> you want. It is also possible to convert back to version 4 after some
> processing.
>
> Matthew McCormack
>
>
> James W. MacDonald wrote:
>> Hi AA,
>>
>> A A wrote:
>>> Hello Everyone,
>>>
>>> I am very new to using R and Bioconductor, so please bare with me.  I
>>> have Affymetrix files that are in CEL format and i am trying to
>>> convert them into text files so that I can work with them.  I have
>>> been trying to use the command justSNPRMA, but I am not sure what to
>>> do after I run the command.  I tried searching on the net to see if
>>> there were step-by-step instructions for doing this, but I have not
>>> been successful.  Would someone direct me to such a site or explain
>>> this process to me?
>>
>> You might want to look at the posting guide, as this message fails to
>> meet even the minimum requirements. Some questions for you:
>>
>> 1.) What kind of Affymetrix files?
>>
>> 2.) What does 'work with them' mean?
>>
>> 3.) What (exact) code have you tried?
>>
>> 4.) What is your output from sessionInfo()?
>>
>> 5.) Who are you (anonymous questions are less likely to be answered)?
>>
>> Best,
>>
>> Jim
>>
>>
>>>
>>> Thanks,
>>>
>>> AA
>>>
>>> _________________________________________________________________
>>> [[elided Hotmail spam]]
>>>
>>> ntrosrchcashback [[alternative HTML version deleted]]
>>>
>>> _______________________________________________ Bioconductor mailing
>>> list Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the
>>> archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>