[BioC] affy & problems with memory
naomi at stat.psu.edu
Fri Jan 13 22:06:31 CET 2006
justRMA in affy is more memory efficient.
At 08:40 AM 1/12/2006, kfbargad at ehu.es wrote:
>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?
> > My apologies for the previous (empty) mail, it slipped me :)
> > > I'm currently working on that chip type myself on a system with
> > > and had to increase the memory assigned to R too. However
> > > "--max-mem-size=1024Mb" seems to be ok in my case. Besides the
> > > how much memory is necessary for the hgu133plus2 maybe somebody
> > > could answer me this two related questions:
> > > * I'm running R under WinXp AND under Linux on the same machine.
> > > 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
> > (finding memory on your local harddrive) then Windows (the /swp
> > filesystem).
> > > * With my 512MB RAM system the old maximum memory value under
> > > 512MB. Is this just a coincidence or does this maximum value rise
> > > if I upgrade my system to 1024MB RAM?
> > No, this is not a coincidence since the maximum value is related to
> > amount available on your system.
> > Cheers,
> > R.
> > _______________________________________________
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