[BioC] Try to run a lots of chips: 32 bits vs 64 bits

[Rafael A. Irizarry]

one way to get around it is to write a function that does RMA but 
reads only the PMs. If you learn R it wont be that
hard. reading only the PMs will reduce the memory use 
by more than 1/2. RMA doesnt use MMs. if you decide to do this, 
email me and ill help as
long as you contribute the final product.

another, less satisfying, way is to run rma by parts (half and half) 
and then join the exprSets.



On Tue, 4 Mar 2003, Laurent Gautier wrote:

> (I've seen answers to this post by Robert & Ben)
> 
> On Mon, Mar 03, 2003 at 02:33:31PM -0800, Shi, Tao wrote:
> > 
> > I'm trying to follow up on the discussions by Laurent and Issac, b/c we're also trying to run a lots of arrays (~200 133A) with Bioconductors.  We tried with R on our 32 bits Linux server with 2G ram and it failed.  So, my questions are:
> > 1) now what is the highest number of chips you can process with Bioconductor?
> 
> It depends on the type of the chips (they were not created equal,
> some are bigger than other). I recently processed 142 U95Av2 on
> a 2Gb linux box.
> 
> ...but 200 133A appears a bit too much to me...
> 
> > 2) How do you know if your R is 32 bits or 64 bits and how do you build 64 bits R under a 32 bits architecture?  Our system administrator mentioned to me that the only mention in the administration manual is for Sparc systems (64-bit
> > arch).
> 
> R can be built for 64 bits (Isaac did so). You may want to 'google' about your
> harware, linux and 64 bits..
> 
> > 3) For specific analyses, for example, quantile normalization and RMA, is there a way around it?
> 
> for the moment, the only I can think of is to crank up your favorite editor
> and try to make your way through... sorry..
> 
> 
> 
> > Many thanks in advance,
> > ...Tao 
> >  
> > 
> > 
> > 
> > ---------------------------------
> > 
> > 
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> > 
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> -- 
> --------------------------------------------------------------
> currently at the National Yang-Ming University in Taipei, Taiwan
> --------------------------------------------------------------
> Laurent Gautier			CBS, Building 208, DTU
> PhD. Student			DK-2800 Lyngby,Denmark	
> tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent
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