[BioC] reading many affy U133 Plus_2.0

[James W. MacDonald]

Yeah, but can he do fitPLM()? I was going to suggest that as well, but 
Henrik's page doesn't mention that as a possibility.

Jim



Mark Robinson wrote:
> David,
> 
> You might have a look at the R package 'aroma.affymetrix' ... you  
> should be able to read/process/analyze 100s of affy chips.  I  
> regularly process >50 exon arrays, which are far larger than U133s.   
> I believe you can do it all in less than 500M RAM.
> 
> Full details are at:
> http://groups.google.com/group/aroma-affymetrix
> 
> Cheers,
> Mark
> 
> 
> On 05/10/2007, at 9:57 PM, <darteta001 at ikasle.ehu.es>  
> <darteta001 at ikasle.ehu.es> wrote:
> 
>> Dear list,
>>
>> In order to normalise my data using fitPLM(), I need to create an
>> affybatch using ReadAffy(). This time I think justRMA() is not an
>> option I can use.
>>
>> Has anyone been successful at reading in a large group of Plus chips
>> (say 100) using ReadAffy() and the normalise them using fitPLM() on
>> a "normal" PC on Windows? What amount of memory is needed for it?
>> Any examples on how many chips you might have loaded with memory
>> details would be very appreciated.
>>
>> Regards,
>>
>> David
>>
>> _______________________________________________
>> 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
> 
> _______________________________________________
> 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

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623