[BioC] affy & problems with memory

[Naomi Altman]

I meant more memory efficient than loading in 
your cel files and then running "rma".  I don't 
know anything about RMA express (and I am sure 
Ben Bolstad's advice is best on this).

--Naomi

At 04:06 PM 1/13/2006, Naomi Altman wrote:
>justRMA in affy is more memory efficient.
>
>--Naomi
>
>At 08:40 AM 1/12/2006, kfbargad at ehu.es wrote:
> >Hi,
> >
> >would it be a solution to use RMAexpress to obtain expression values
> >for a good amount of arrays and then import them into your R session?
> >I haven´t got much experience on this program but it is said on the
> >RMAexpress webpage that the program can process upto 250 arrays
> >simultaneously ( I guess not U133plus) and in the history section it
> >is stated that the 0.4alpha3 version can run 200 arrays.
> >
> >Any information on U133plus?
> >
> >David
> >
> > > My apologies for the previous (empty) mail, it slipped me :)
> > >
> > > > I'm currently working on that chip type myself on a system with
> >512MB RAM
> > > > and had to increase the memory assigned to R too. However
> > > > "--max-mem-size=1024Mb" seems to be ok in my case. Besides the
> >problem of
> > > > how much memory is necessary for the hgu133plus2 maybe somebody
> >out there
> > > > could answer me this two related questions:
> > > > * I'm running R under WinXp AND under Linux on the same machine.
> >However
> > > > there has never been any memory problem in linux. So is the memory
> > > > allocation or the  assignment of the max. memory size that can be
> >used by R
> > > > different in the two systems?
> > >
> > > This is due to the much more flexible memory management of Linux as
> > > opposed to Windows. Theoretical limit on a 32-bit Windows machine as
> > > 2Gb; 4 Gb under Linux. Linux has also a more flexible way of
> >swapping
> > > (finding memory on your local harddrive) then Windows (the /swp
> > > filesystem).
> > >
> > >
> > > > * With my 512MB RAM system the old maximum memory value under
> >WinXP was
> > > > 512MB. Is this just a coincidence or does this maximum value rise
> >to 1024MB
> > > > if I upgrade my system to 1024MB RAM?
> > >
> > > No, this is not a coincidence since the maximum value is related to
> >the
> > > amount available on your system.
> > >
> > > Cheers,
> > > R.
> > >
> > > _______________________________________________
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> > > Bioconductor at stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > >
> >
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>Naomi S. Altman                                814-865-3791 (voice)
>Associate Professor
>Dept. of Statistics                              814-863-7114 (fax)
>Penn State University                         814-865-1348 (Statistics)
>University Park, PA 16802-2111
>
>_______________________________________________
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111