[BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
beniltoncarvalho at gmail.com
Mon Mar 22 12:18:53 CET 2010
I was able to reproduce the issue you reported. The probeNames()
method in 1.10.3 is missing a sort by fid.
res <- dbGetQuery(db(object), "SELECT fsetid FROM
pmfeature ORDER BY fid")[]
I'll get this fixed now.
On Mon, Mar 22, 2010 at 11:04 AM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> 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,
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