[BioC] problem with mva.pairs

[Ben Bolstad]

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 at 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]]
> > 
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> 
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