Search
Question: extracting one probe set
0
gravatar for Thomas Turner
12.8 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 12.8 years ago by James W. MacDonald43k • written 12.8 years ago by Thomas Turner20
0
gravatar for James W. MacDonald
12.8 years ago by
United States
James W. MacDonald43k 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
ADD COMMENTlink written 12.8 years ago by James W. MacDonald43k
James W. MacDonald 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")) This returns a 'list' of objects of class 'ProbeSet'. To get the slot 'pm', there is no accessor function. One must use the '@' operator. ### R example ps <- probeset(affybatch, genenames = ("probe set name")) ## return the 'pm' for the first probe set ps[[1]]@pm ## return the 'pm' for all the probe sets lapply(ps, function(x) x@pm) > > Probably an easier method is to simply use the pm() and mm() accessor > functions. ...depends on what one wants to do... ...having things stored in a ProbeSet can let one use a couple of plotting methods, or 'express.summary.stat'... L. > 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 > > >
ADD REPLYlink written 12.8 years ago by lgautier@altern.org950
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 254 users visited in the last hour