[BioC] Affy Normalization!

[Puhong Gao]

Rafael,

Thank you very much for your input. I thought that, though quantile
nomalization only uses pm values by default, it will read in both pm and mm
values.

I would love to test justRMA. But here is my dilemma. justRMA function is
available in R; but I have tried unsuccessfully to get the 150 cel files
into R. I managed to get the 150 cel files read into S-Plus ArrayAnalyzer
(no problem); but justRMA is not included in the ArrayAnalyzer. Any
suggestions? Is it possible to somehow port justRMA function to S-plus?
Thanks.

Regards,

Puhong

----- Original Message -----
From: "Rafael A. Irizarry" <ririzarr at jhsph.edu>
To: "Puhong Gao" <pgao at hunter.cuny.edu>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Tuesday, June 10, 2003 1:45 PM
Subject: Re: [BioC] Affy Normalization!


> 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
> > [[alternate HTML version deleted]]
> >
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>