[BioC] memory bottleneck on Linux

[Ben Bolstad]

I am surprised that you can not get 100 CEL files to run successfully. 4
GB (on a single machine) should be more than sufficient to do this.
Because the MAS5 method is not a multi-chip method, you could compute
the expression measures in smaller groups (say groups of 25 for
example).  Join the expression measures together for each group and then
scale them appropriately.

If you are using the mas5() function from the affy package remember to
set normalize=FALSE when doing each of the groups (so as not to scale
the groups individually).

Ben


On Wed, 2003-07-02 at 09:52, Tapan Mehta wrote:
> Hello,
> 
> I am trying to run a task of 100 CEL files each of 10
> MB on Linux based Bewoulf cluster with each node of  4
> GB. I am trying to use the mas5 method in the affy
> library. However I am unable to finish it gives memory
> problems. I am unable to increase the memory as the
> function of memory in R is only for Windows( as posted
> on the R mailing list). Please could anybody guide me
> in this problem? 
> 
> Regards,
> 
> Tapan Mehta
> 
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-- 
Ben Bolstad <bolstad at stat.berkeley.edu>
http://www.stat.berkeley.edu/~bolstad