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

[James W. MacDonald]

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