[BioC] invariant set normalisation

[Al Ivens]

Sally,

I am assuming you are using R/bioc installed in a 32bit Windows
envoroment?

If so, the largest amount of memory that can physically be accessed is
4Gb (whether that is "proper" RAM or a pagefile on disk).  The only way
you can get more than that is to get a 64bit computer, or as Seth
suggests, use a different operating system that doesn't have the tedious
constraints that the Windows OS does.

To tell R you want to use as much RAM as possible in a 32bit Windoze
enviroment, just type:

memory.limit(size=4000)

at the beginning of whatever you are trying to do (i.e. on opening the
session) (or put it in Rprofile).

This is what I get (R2.3.0, Windows GUI):

> memory.limit(size=4000)
NULL
> memory.limit()
[1] 4194304000

The pagefile manager within windows will deal with the rest.  It does,
of course, assume that the total of virtual and physical RAM can get as
high as 4Gb (i.e. you have that amount of disk space + installed RAM)!

No guarantees, but it should help.

a

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Sally-Ann Walford
> Sent: 26 April 2006 13:48
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] invariant set normalisation
> 
> 
> I am attempiting to use the cond.norm function in the smida 
> package to normalise 30 cDNA dual channel arrays with 
> approximately 15000 spots per array. I chose the quantile 
> function using and invariant set =100. 
> Unfortunately I keep getting the following error message 
> "Error: cannot allocate vector of size 207900 Kb".  does 
> anyone know what this means?
> 
> Kind regards
> Sally
> 
> Sally-Ann Walford
> Dept. Molecular and Cell Biology
> UCT
> 
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