[BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
beniltoncarvalho at gmail.com
Mon Mar 22 12:04:36 CET 2010
what's the array you're looking at?
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:
> workingDir = getwd();
> pms = pm(rawdata)
> res <- dbGetQuery(db(rawdata), "SELECT fsetid,atom,fid FROM pmfeature")
> 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:
>  818005
>  818005
> # first value in probe names
>  "7896737"
> # first value in pm indices
>  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,
More information about the Bioconductor