[BioC] affy & problems with memory

Roel Verhaak r.verhaak at erasmusmc.nl
Wed Jan 11 22:33:27 CET 2006

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 

> * 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.


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