[BioC] Affy Normalization!

[Rafael A. Irizarry]

thats what quantile normalization does by default. to get the pms use the 
method: pm

the function justRMA uses only pms and takes advantage of this to save on 
memory. you can look at the code for some hints.

On Tue, 10 Jun 2003, Puhong
Gao wrote:

> Hi, all,
> 
> To reduce the data size before quantile normalization, I am thinking to 
take PM intensity only (to solve memory problem).  Is there a way to 
separate pm and mm data while the affybatch format is still perserved? If 
yes, is it appropriate to normalize the data based on the PM values only? 
Thanks in advance for your inputs.     
> 
> Data: from 150 u34a chips   Computer: Windows XP pro with 2 GB of RAM
> 
> Regards,
> 
> Puhong Gao, PhD
> Dev. Psychobiology
> NYSPI, Unit# 40
> 1051 Riverside Dr.
> New York, NY 10032
> (212) 543-5710
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