[BioC] RMA on a batch with NA values

[James W. MacDonald]

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:

http://article.gmane.org/gmane.science.biology.informatics.conductor/4258/match=,

Best,

Jim


> 
> Thanks,
> Adi L. Tarca
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
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