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

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James Perkins ▴ 120

@james-perkins-4948

Last seen 9.6 years ago

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 [[alternative HTML version deleted]]

probe oligo probe oligo • 1.3k views

ADD COMMENT • link updated 11.2 years ago by James W. MacDonald 65k • written 11.2 years ago by James Perkins ▴ 120

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 3 hours ago

United States

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

ADD COMMENT • link 11.2 years ago James W. MacDonald 65k

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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 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 11.2 years ago Benilton Carvalho ★ 4.3k

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