[BioC] RMA on a batch with NA values

[Tarca, Adi]

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?

Thanks,
Adi L. Tarca