I put a newer much more optimised version of mva.pairs() into the development affy package last week. You should find this much nicer. Ben On Thu, 2004-03-04 at 10:39, Johannes Freudenberg wrote: > Francesca, > > I don't remember that my R session actually crashed. I think, it just takes > forever. Therefore I randomly select a subset of, say, 10,000 PMs and use this > subset instead: > > index <- sample(1:(dim(pm(myAffyData))[1]), 10000) > mva.pairs(pm(myAffyData)[index,]) > > I don't think it's necessary or even helpful to use all 200,000 PMs for the MvA > plots. > > Best, > Johannes > > > Quoting Francesca Buffa <buffa@gci.ac.uk>: > > > Dear all, > > > > > > > > When I try to use the function mva.pairs applied to pm("myAffyData") I > > never > > manage to produce an outcome and my RGui section stops running. I'm > > using R > > 1.8.1 in the window version. The "myAffyData" is an AffyBatch object > > with > > dimension of about 712x712 features (11885 kb). When I try the same on > > a > > smaller file I don't have any problems; however I've monitored the > > memory/CPU usage during the big run (where my RGui section crashes) and > > I > > never reach my memory or CPU limits during the run (in fact I'm far > > below). > > Has anyone encountered a similar problem? Is there a limit in the file > > dimensions with mva.pairs? Any help that you can give would be very > > much > > appreciated. > > > > > > > > Thank you, > > > > > > > > Francesca > > > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor