[BioC] memory requirement

[Laurent Gautier]

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	
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