[BioC] how to solve the memory problem in RMA if I want to get probe level expression?

James W. MacDonald jmacdon at med.umich.edu
Fri May 4 18:18:54 CEST 2007

Hi James,

James Anderson wrote:
> I am now trying to get the probe level values from RMA, since I want to adjust 
> the batch effect in probe level instead of probe set level. However, 
> justRMA seems to do everything until the probe set level. What I want to do 
> is to use RMA to obtain probe level expression matrix, then adjust the batch 
> effect, then using median polish to get probe set level. 
> Does anybody know how to circumvent the memory problem if 
> I only want to get the probe level matrix? 

Why exactly do you want to adjust for batch at the probe level? The 
batch effect will be a per-chip effect, so I wouldn't imagine that 
adjusting at the probe level would be that much different, except for 
the fact that you would be doing things pre-medianpolish, so any 
outliers could really skew things.

Anyway, if you are limited by RAM I don't think you will be able to do 
really fancy things. I would recommend either increasing the amount of 
RAM you have, or finding a computer that has enough. If you want to do 
probe-level modeling you should be using the affyPLM package which IIRC 
doesn't have any methods explicitly designed to use minimal amounts of RAM.



> Many thanks,
> James
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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