[BioC] Exclude individual probes before normalization

[James W. MacDonald]

Hi Jenny,

I have never needed to use the subset argument, so don't know for sure. 
However, the subsetting appears to be done at the C level rather than at 
the R level, so I would bet there isn't much copying being done, which 
is the only way I know that more memory would be required. My bet is 
that it would take less memory.

Ben Bolstad would know for sure, since he wrote the C code.

Best,

Jim



Jenny Drnevich wrote:
> Hi Jim,
> 
> Do you know if using the 'subset' argument of rma() has any effect on the 
> memory it uses? I'm not sure if it would decrease the memory requirements 
> by working with less data, or actually increase it by doing a subsetting 
> step somewhere.
> 
> Thanks,
> Jenny
> 
> At 07:37 AM 9/9/2006, James W. MacDonald wrote:
> 
>>Dana Wohlbach wrote:
>>
>>>Does anyone know of a way to exclude individual probes before
>>>normalizing using a method like RMA?  In other words, I have
>>>identified certain probes in my CEL files that I don't want included
>>>in the normalization procedure.  Is there a way to use Bioconductor
>>>to make this happen?
>>
>>See ?rma(), in particular the 'subset' argument.
>>
>>Best,
>>
>>Jim
>>
>>
>>
>>>Thanks,
>>>Dana
>>>
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>>
>>http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>>--
>>James W. MacDonald
>>University of Michigan
>>Affymetrix and cDNA Microarray Core
>>1500 E Medical Center Drive
>>Ann Arbor MI 48109
>>734-647-5623
>>
>>
>>
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> 
> 
> Jenny Drnevich, Ph.D.
> 
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
> 
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
> 
> ph: 217-244-7355
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> e-mail: drnevich at uiuc.edu
> 
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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
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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