[BioC] Affy Normalization!

[Rafael A. Irizarry]

you might want to try it again avoiding the use of ReadAffy or 
read.affybatch. by never creating an AffyBatch and reading only a pm 
matrix you make a  smaller object. as pointed out by james, this is what 
justRMA does. 

if you want RMA values and dont necesarily want to work within 
R/Bioconductor you might consider using:

http://stat-www.berkeley.edu/users/bolstad/RMAExpress/RMAExpress.html

On Tue, 10 Jun 2003, Puhong Gao 
wrote:

> 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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> > >
> >
> 
>