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

[Benilton Carvalho]

what's the array you're looking at?

sessionInfo()?

thanks,
b

On Mon, Mar 22, 2010 at 10:54 AM, Mikhail Pachkov <pachkov at gmail.com> wrote:
> 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
>