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Question: extracting one probe set
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13.8 years ago by
Thomas Turner20 wrote:
Dear all, I am trying to simply extract a table with the probe intensities for a probe set that I specify by name. As described in 6.2 of the manual, I have been trying to use this command: ps <- probeset(affybatch, genenames = ("probe set name")) However, I am unable to make the following command work: pm(ps[[1]]) If I ask R about my "ps", it gives me this: $"Ag.X.66.0 CDS s at" ProbeSet object: id=Ag.X.66.0 CDS s at pm= 1 probes x 1 chips My affybatch includes four chips, which do not seem to be what this is telling me. I am new to R, and any advice would be warmly received. Thank you, Tom Turner ADD COMMENTlink modified 13.8 years ago by James W. MacDonald46k • written 13.8 years ago by Thomas Turner20 0 13.8 years ago by United States James W. MacDonald46k wrote: Thomas Turner wrote: > Dear all, > > I am trying to simply extract a table with the probe intensities for a > probe set that I specify by name. As described in 6.2 of the manual, I > have been trying to use this command: > > ps <- probeset(affybatch, genenames = ("probe set name")) Probably an easier method is to simply use the pm() and mm() accessor functions. pm(affybatch, genename) mm(affybatch, genename) HTH, Jim > > However, I am unable to make the following command work: > > pm(ps[[1]]) > > If I ask R about my "ps", it gives me this: > >$"Ag.X.66.0 CDS s at" > ProbeSet object: > id=Ag.X.66.0 CDS s at > pm= 1 probes x 1 chips > > My affybatch includes four chips, which do not seem to be what this is > telling me. I am new to R, and any advice would be warmly received. > > Thank you, > > Tom Turner > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109