[BioC] affy & problems with memory

[Naomi Altman]

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.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor

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