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

[Benilton Carvalho]

btw, the following is faster:

setMethod("probeNames", "GeneFeatureSet",
                 function(object, subset=NULL){
                   res <- dbGetQuery(db(object), "SELECT fid, fsetid
FROM pmfeature ORDER BY fid")
                   idx <- order(res[["fid"]])
                   as.character(res[idx, "fsetid"])
                 })

b

On Mon, Mar 22, 2010 at 11:18 AM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> Dear Mikhail,
>
> I was able to reproduce the issue you reported. The  probeNames()
> method in 1.10.3 is missing a sort by fid.
>
> setMethod("probeNames", "GeneFeatureSet",
>                 function(object, subset=NULL){
>                   res <- dbGetQuery(db(object), "SELECT fsetid FROM
> pmfeature ORDER BY fid")[[1]]
>                   as.character(res)
>                 })
>
> I'll get this fixed now.
>
> b
>
> On Mon, Mar 22, 2010 at 11:04 AM, Benilton Carvalho
> <beniltoncarvalho at gmail.com> wrote:
>> 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
>>>
>>
>