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

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

-- 
Dr James R Perkins
Institute of Structural and Molecular Biology
Division of Biosciences
University College London
Gower Street
London, WC1E 6BT
UK

email: j.perkins@ucl.ac.uk

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