[BioC] memory usage ReadAffy() and probe level information

Arne.Muller at aventis.com Arne.Muller at aventis.com
Tue Apr 6 14:54:58 CEST 2004


I'd interested in a solution myself ;-) .

Reading in many cel files is actually not the bottle neck! When it comes to
use "expresso" with normalisation across the cel files the memory usage
increases again, and you may eventually exceed all your 2GB of memory. I'm
normalizing 42 MG-U74Av2 chips and expresso takes about 800mb for rma +
quntiles + pmonly + medianpolish.

It was mentioned previously in this list (don't remember when exactly) the
justRMA method performs exactly the above normalization procedure, but is a
lot fasdte rand used a lot less memory. You feed the cel file names to the
routine not an AffyBath object (see help(justRMA)).

Off course if you'd like to use other normalization of background correction
methods you're pretty much bound to use expresso, for which will probably
need too much memory for your 100 cel files ...

Sorry, I've not suggestion for your 2nd problem (probe set location).



Arne Muller, Ph.D.
Toxicogenomics, Aventis Pharma
arne dot muller domain=aventis com

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of 
> Roel Verhaak
> Sent: 06 April 2004 14:32
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] memory usage ReadAffy() and probe level information
> Hi,
> I have two questions regarding the use of the affy package:
> - I have a large series of cel-files and am trying to read
> them at once. Unfortunately, the ReadAffy-function seems to
> use a lot of memory. My workstation has 2 Gig of RAM
> installed, but trying to read >100 cel-files (HGU133a) is a
> no-go. This is R1.8.1 with Bioconductor 1.3 on a Windows
> machine. Reading in 50 cel-files already means a
> (peak-)memory usage of 800 meg. Is there any solution to
> this, because I would like to read 300 cel-files at the same
> time if possible. I have played around with the
> memory.limit()-function, but with no success.
> - Second, after data import I would like to retrieve all
> information on a probe level for several probe sets. I do
> this using the pm()-function, for instance
> >pm(CelFiles)[1:16, 1:50]. The problem is that I have to find 
> out first where which exact "location" the probe set of 
> interest has. This is not a big problem, but I thought there 
> might be a more elegant solution to this. 
> Thanks in advance,
> Roel Verhaak

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