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

Laurent Gautier laurent@cbs.dtu.dk
Tue, 4 Mar 2003 02:05:17 +0100

(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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currently at the National Yang-Ming University in Taipei, Taiwan
Laurent Gautier			CBS, Building 208, DTU
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