[BioC] affy & problems with memory

kfbargad@ehu.es kfbargad at ehu.es
Thu Jan 12 14:40:10 CET 2006


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 
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. 
> > 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 
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 
> amount available on your system.
> Cheers,
> R.
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