[BioC] Oligo - oligo::probeNames() returns transcript clusters, not probe sets

[Benilton Carvalho]

Thanks, Jim,
I'll address the doc issue ASAP.
benilton

2013/1/29 James W. MacDonald <jmacdon at uw.edu>:
> Hi James,
>
>
> On 1/29/2013 9:47 AM, James Perkins wrote:
>>
>> Hi all,
>>
>> I've just noticed a possible bug in oligo. When using oligo::probeNames to
>> return the probeset mappings for the probes in the unprocessed
>> GeneFeatureSet, in older versions we obtain the probeset ids
>
>
> Not a bug, but there is some missing documentation. Benilton recently added
> the 'target' argument to most if not all accessors, so you have to specify
> what you want (unless of course you want the default of 'core').
>
>> head(probeNames(dat))
>
> [1] "10529921" "10423731" "10338032" "10603809" "10486041" "10341702"
>> head(probeNames(dat, target = "probeset"))
>
> [1] "10529922" "10423732" "10338032" "10603810" "10486052" "10341702"
>
> Best,
>
> Jim
>
>
>
>>
>> However in R-2.15.1 (and also in the latest version of R, though not
>> shown)
>> we appear to be obtaining transcript cluster ids:
>>
>> R version 2.15.1 (2012-06-22)
>>
>> oligo::probeNames(affyGeneFS)[1:10]
>>   [1] "10529921" "10423731" "10338032" "10603809" "10486041" "10341702"
>>   [7] "10380303" "10379387" "10359908" "10578806"
>>
>>
>> R version 2.12.2 (2011-02-25)
>>
>>> oligo::probeNames(affyGeneFS)[1:10]
>>
>>   [1] "10529922" "10423732" "10338032" "10603810" "10486052" "10341702"
>> "10380312" "10379388" "10359913" "10578809"
>>
>> Not sure if this is a bug or intended change of behaviour, if it is the
>> latter, is there a way to get the probe set names? oligo::probesetNames
>> doesn't appear to be what I'm after, since the result don't match the rows
>> of pm(GeneFeatureSet).
>>
>> Thanks for your help!
>>
>> Jim
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
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