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

[Benilton Carvalho]

don't change the probeNames method.

Use probeNames() to get the (character version) of fsetid and
pmindex() to get the fid.

b

On Mon, Mar 1, 2010 at 4:50 PM, Mikhail Pachkov <pachkov at gmail.com> wrote:
> 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
> pmfeature")
>                   paste(res[,1],res[,2])
>                 })
>
> Could you tell me if that is correct way to get fid, fsetid pairs for pms?
>
> Thank you in advance.
>
> Best regards,
>
> Mikhail
>