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

Mikhail Pachkov pachkov at gmail.com
Mon Mar 1 17:50:16 CET 2010

On Mon, Mar 1, 2010 at 12:06 PM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> my bad... that's a mod that never made it to the code... in the
> meantime, can you please run the following bit once (which will set
> probeNames and after which everything will be fine):
> setMethod("probeNames", "GeneFeatureSet",
>                  function(object, subset=NULL){
>                    res <- dbGetQuery(db(object), "SELECT fsetid FROM
> pmfeature")[[1]]
>                    as.character(res)
>                  })

That works. Thank you! However I need both fsetid and fid so I tried
to modify the method a little:

setMethod("probeNames", "GeneFeatureSet",
                 function(object, subset=NULL){
                   res <- dbGetQuery(db(object), "SELECT fid,fsetid FROM

Could you tell me if that is correct way to get fid, fsetid pairs for pms?

Thank you in advance.

Best regards,


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