[BioC] memory bottleneck on Linux

[Tapan Mehta]

I tried using rma instead of mas5 to check whether the
memory restrictions still apply. Unfortunately they do
apply and right now I am finding it impossible to
process all the 100 files together. However mas5 works
for smaller batch of 20 or 25 chips. However it would
be great to figure out a solution that can process 100
files since for rma I need to process all the 100
files in a single batch. Are these
algorithms(mas5,rma) parallelizable or can the
programs be modified for making the optimum use of the
cluster?

--- Ben Bolstad <bolstad at stat.berkeley.edu> wrote:
> 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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> > Bioconductor at stat.math.ethz.ch
> >
>
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> -- 
> Ben Bolstad <bolstad at stat.berkeley.edu>
> http://www.stat.berkeley.edu/~bolstad
>