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

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Fri May 4 17:59:24 CEST 2007

It is pretty unclear to me what you are trying to accomplish. The RMA  
procedure consists of background subtraction (on a per chip level),  
quantile normalization (all chips together, probe level) and  
summarization. Are you talking about quantile normalization? And do  
you then want to do this on the probeset level instead of the probe  


On May 4, 2007, at 8:35 AM, 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?
> Many thanks,
> James
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