[BioC] Blobs

[Mark Cowley]

Hi Steve and Kasper,
Using affxparser would keep things in R/Bioconductor, but there is  
also apt-cel-convert from the Affymetrix Power Tools
http://www.affymetrix.com/support/developer/powertools/changelog/index.html

cheers,
Mark

On 15/07/2008, at 4:00 AM, Kasper Daniel Hansen wrote:

> Use affxparser
>
> Kasper
>
> On Jul 14, 2008, at 7:42 AM, Steve Lianoglou wrote:
>
>> Hi Mark,
>>
>> On Jul 13, 2008, at 6:58 PM, Mark Cowley wrote:
>>
>>> There's also MblobR.
>>> reference:
>>> Song, J. S.; Maghsoudi, K.; Li, W.; Fox, E.; Quackenbush, J. &  
>>> Liu, X. S.
>>> Microarray blob-defect removal improves array analysis.
>>> Bioinformatics, 2007, 23, 966-971
>>
>> I just downloaded this to check it out ... have you been using it  
>> all? After downloading all the dependency jars[1], I realized that  
>> it only opens CEL files saved as version 4 (the binary one), while  
>> the files I have are version 3[2].
>>
>> Do you (or anybody else) know if there is an easy way to convert  
>> between versions of CEL files?
>>
>> Thanks,
>> -steve
>>
>> [1] For anybody else who's trying to run this, you'll need to have  
>> in your classpath:
>> * junit.jar: http://junit.org/
>> * swing-layout.jar: https://swing-layout.dev.java.net/
>>
>> [2] Affy cel version info: http://www.stat.lsa.umich.edu/~kshedden/Courses/Stat545/Notes/AffxFileFormats/cel.html
>>
>> --
>> Steve Lianoglou
>> Graduate Student: Physiology, Biophysics and Systems Biology
>> Weill Cornell Medical College
>>
>> http://cbio.mskcc.org/~lianos
>>
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>