[BioC] masking probe pairs in RMA

[Lana Schaffer]

Greetings,
I have masked 168 probe pairs and then run RMA and Alot of the expression values have come out NA.
I am concluding that RMA is not calculating the expression values for probesets which contain masked
probepairs.  Is this a correct conclusion?

abatch <- bg.correct.rma(abatch0);
msk <- scan(filename, skip=0, list("", ""))
for (i in 1:length(msk[[1]])) { 
nam <- msk[[1]][i]; 
txt <- gsub("-", ":", msk[[2]][i]); 
lst <- eval(parse(text=paste("c(", txt, ")"))); #list
if (i == 1) { 
ids <- pmindex(abatch, nam)[[1]][lst]; 
} else { 
ids <- c(ids, pmindex(abatch, nam)[[1]][lst]); 
} 
ids <- c(ids, mmindex(abatch, nam)[[1]][lst]); 
} 
intensity(abatch)[ids, ] <- NA; 
eset2 <- rma(abatch,background=F);

Thanks for any help.
Lana
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