[BioC] memory requirement

Liaw, Andy andy_liaw@merck.com
Tue, 26 Nov 2002 08:01:09 -0500


If you've upgraded to R-1.6.1, note that the limit on Windows has been
raised to the smaller of physical RAM and 1GB (used to be 256MB).  So unless
you have more than 1GB of RAM, there's no need to do that.

Andy

-----Original Message-----
From: Stephen Henderson [mailto:s.henderson@ucl.ac.uk]
Sent: Tuesday, November 26, 2002 6:52 AM
To: 'Laurent Gautier'
Cc: 'bioconductor@stat.math.ethz.ch'
Subject: RE: [BioC] memory requirement



Here is the advice given to me on improving R memory on Win some time ago on
this very list from --Tibor van. This helped a bit.

If you have a shortcut on your desktop for R (or somewhere else), then if
you right click on the icon and bring up the Properties window, you will see
an entry for 
Target with the path to the executable filled in. After that path (and
outside of the quotes) add this command-line argument on my PC, for example
it would look like this: 

 

"C:\Program Files\R\rw1051\bin\Rgui.exe" --max-mem-size=768M 

 

Restart R and you will be in business...

Stephen Henderson
Wolfson Institute for Biomedical Research
UCL, London




-----Original Message-----
From: Laurent Gautier [mailto:laurent@cbs.dtu.dk] 
Sent: Tuesday, November 26, 2002 12:57 AM
To: Wilkinson, Mark
Cc: 'bioconductor@stat.math.ethz.ch'
Subject: Re: [BioC] memory requirement

On Mon, Nov 25, 2002 at 03:43:08PM -0600, Wilkinson, Mark wrote:
> Here, here.  I'd've asked sooner, but suspected I'd be advised the brute
> force approach of beefing up my machine.
> 
> I'm running the affy package, specifically, with U133 chips, but am only
> able to read in 10-15 CEL files at once.  Any way around this?  I've
> considered using 'merge' to read a few, merge, read a few more, merge,
etc.
> I'm using Windows R, which seems to have poor memory management anyway.
Any
> tips?
> 

How much memory did you have ?

I do not know much of the behavior with Windows, but with linux I remember
doing
the full monty (raw data -> normalization -> summary expression value) for
about 80 U95A at once on a machine with 2Gb.

note : the new release of the package spits out something with the size of
the 'AffyBatch' object with the default print method (try:
data(Dilution)
Dilution
)
 
Hopin' it helps,


L.


> 
> Mark Wilkinson
> Informatics Analyst
> St. Jude Children's Research Hospital
> Department of Pharmaceutical Sciences
> 
> 
>  -----Original Message-----
> From: 	Yi-Xiong Zhou [mailto:yzhou@arcturusag.com] 
> Sent:	Monday, November 25, 2002 3:24 PM
> To:	'bioconductor@stat.math.ethz.ch'
> Subject:	[BioC] memory requirement
> 
> I am concerning the memory requirement of running bioconductor on Affy
> chips. Could you give me an estimate?
> 
> Thanks. 
> 
> Yi-Xiong
> 
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-- 
--------------------------------------------------------------
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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