[BioC] {Spam?} Re: RMA on a batch with NA values

Tarca, Adi atarca at med.wayne.edu
Mon Aug 11 18:50:48 CEST 2008

Thanks Jim,

It looks like rma has an argument "subset" that allows me to choose the
probesets that I want to consider.
Even discarding some probes out of the considered probesets can work as
well if no background correction is required, i.e.
esetb<-rma(abatch,subset=psok, background=FALSE) 

 works fine after inserting Nas.

I just find strange that the background correction step requires that
all probe intensities should be valid number and not contain any Nas.


Adi Laurentiu TARCA, Ph.D. 
Research Associate, Dept. of Computer Science &
Services in Support of the NIH Perinatology Research Branch,
Manager of the Bioinformatics Core, Karmanos Cancer Institute,
Wayne State University, 
3990 John R., Office 4809,
Detroit, Michigan 48201
Tel: 1-313-5775305 
Cell: 1-313-4043116 

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Monday, August 11, 2008 9:05 AM
To: Tarca, Adi
Cc: bioconductor at stat.math.ethz.ch
Subject: {Spam?} Re: [BioC] RMA on a batch with NA values

Hi Adi,

Tarca, Adi wrote:
> Hi all,
> I am trying to run RMA using only a limited number of probes. I have 
> the x and y coordinates of those probes that I want to use.
> The approach I have tried was to replace with NA all probe intensities

> that I want to discard, but the RGUI gives an error and tries to end 
> the session. The console is still running but it does not return any 
> results.
> Here is the code I use:
> #####
> abatch<-ReadAffy(filenames=fnss,celfile.path="./CELL")
> indok<-xy2indices(x=okx,y=oky,abatch=abatch)
> ints<-intensity(abatch)
> ints[-indok,]<-NA
> intensity(abatch)<-ints
> esetb<-rma(abatch)
> Any ideas?

You won't be able to just set things equal to NA in order to remove them
from consideration.

There is some code that Ariel Chernomoretz posted back in '05 that might
still work to remove particular probes from a probeset:




> Thanks,
> Adi L. Tarca
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James W. MacDonald, M.S.
Hildebrandt Lab
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646

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