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 > > >