Hi

More information:
1,50 GB RAM

> sessionInfo()
R version 2.4.0 (2006-10-03) 
i386-pc-mingw32 

locale:
LC_COLLATE=Norwegian (Bokmål)_Norway.1252;LC_CTYPE=Norwegian (Bokmål)_Norway.1252;LC_MONETARY=Norwegian (Bokmål)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokmål)_Norway.1252

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets" 
[7] "base"     


From the runing of the script:
> library(limma)
> library(affyQCReport)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: affy
Loading required package: affyio
Loading required package: simpleaffy
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Welcome to 'affyQCReport' V 1.6-1
Further information available at: www.bifix.org
      mailto: craig.parman@bifix.org
> library(RColorBrewer)
> library(xtable)
> library(simpleaffy)
> memory.limit(4000)
NULL
> dataSet <- read.affy()
Error: cannot allocate vector of size 381064 Kb

Hopes this helps.

Ingrid

---
Ingrid H.G. Østensen
Bioinformatics user support (NMC)
Department of Tumor Biology (Montebello)
Rikshospitalet-Radiumhospitalet Medical Center
0310 Oslo

E -mail: ingrid@microarray.no
Phone:  +47 22 93 54 11
Fax:  +47 22 52 24 21



-----Original Message-----
From: Sean Davis [mailto:sdavis2@mail.nih.gov]
Sent: Mon 12/11/2006 15:42
To: bioconductor@stat.math.ethz.ch
Cc: Ingrid H. G. Østensen
Subject: Re: [BioC] Compare results from different analysis (Affymetrix)
 
On Monday 11 December 2006 09:33, Ingrid H. G. Østensen wrote:
> Hi
>
> I am currently working on data from the Affymetrix platform. I have gotten
> 36 arrays that are divided into 3 groups: 3 different cell lines where two
> are derived/changed versions of the first. These 3 groups are divided into
> 4 time points: 0 (control), and 3, 24 and 72 hours. There are 7 comparisons
> that are to be done: One for each group (3) and one for each time point
> (4).
>
> Because this is the Human Genome U133 Plus 2 Array from Affymetrix I can
> not read all the files into R/Bioconductor at once, I run out of memory. I
> can divide the files into the different comparisons groups and work on
> these but it is one thing that troubles me. If I do the seven different
> comparisons (everything separate: loading the data, normalization, analysis
> etc) can I compare the different results? For example: Lock at time point
> 24 and 72 to find the differences between them, or cell group 1 and 2?

Hi, Ingrid.  You might start by letting us know how you are trying to load the 
arrays into Bioconductor.  There may be a way to load all of them (by using 
justRMA instead of RMA, for example).  Include the output of sessionInfo() so 
that we know the OS and R version, as well as the amount of RAM in your 
machine.  If you can load all the arrays simultaneously, it may make your 
life easier down the road.

Sean



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