Question: problem with mva.pairs
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gravatar for Francesca Buffa
15.5 years ago by
Francesca Buffa20 wrote:
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]]
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ADD COMMENTlink modified 15.5 years ago by mai98ftu@studserv.uni-leipzig.de140 • written 15.5 years ago by Francesca Buffa20
Answer: problem with mva.pairs
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gravatar for Rafael A. Irizarry
15.5 years ago by
Rafael A. Irizarry2.3k wrote:
the problem is mva.pairs runs a loess for each pair which can be very time consuming in R. if this is happening i would recommend making your own mva.pairs... also, if any user out there has something better than the current implementation of mva.pairs, please contact me offline to discuss the possibility of including it in the affy package. On Wed, 3 Mar 2004, Francesca Buffa wrote: > 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 >
ADD COMMENTlink written 15.5 years ago by Rafael A. Irizarry2.3k
Answer: problem with mva.pairs
0
gravatar for mai98ftu@studserv.uni-leipzig.de
15.5 years ago by
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 >
ADD COMMENTlink written 15.5 years ago by mai98ftu@studserv.uni-leipzig.de140
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
ADD REPLYlink written 15.5 years ago by Ben Bolstad1.1k
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