[BioC] problem with mva.pairs

[Johannes Freudenberg]

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
> 
>  
> 
>  
> 
> 
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> 
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