[BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene

[Mikhail Pachkov]

Dear Benilton,

I have got a problem obtaining probe indices along with probe names. My script:

library(oligo);
workingDir = getwd();
celfiles<-list.files(path=workingDir,pattern=".CEL$|.cel$");
rawdata=read.celfiles(celfiles);

pms = pm(rawdata)
rmadata=rma.background.correct(pms)
qndata=normalize.quantiles(log2(rmadata))

res <- dbGetQuery(db(rawdata), "SELECT fsetid,atom,fid FROM pmfeature")
pid=paste(res[,1],res[,2],res[,3],sep=":")
rownames(qndata)<-pid

colnames(qndata)<-sampleNames(rawdata)

However during analysis of the data it looked like probe names were
determined wrong. I have tried to use pmindex() to extract "fid" of pm
probes which seems to be a list of numbers sorted in ascending order.
I do the following:

pnames=probeNames(rawdata)
length(pnames)
[1] 818005

pmidx=pmindex(rawdata)
length(pmidx)
[1] 818005

# first value in probe names
pnames[1]
[1] "7896737"

# first value in pm indices
pmidx[1]
[1] 1056

If I check pgf file for probe with index "1056", it belongs to
probeset "7981328" not "7896737" as it given in pnames.

My question: How to obtain probeset-probe_id pairs in correct order
for annotating expression values in "pms" matrix?

Best regards,

Mikhail