[BioC] memory to use affy package

[Laurent Gautier]

On Fri, Sep 06, 2002 at 04:20:52PM +0100, Stephen Henderson wrote:
> I have been trying to use the affy package. I am running the Win32 version
> but I am finding that calculating expression values (HG133A X 6) crashes R.
> that is I run out of memory. 
> 
> e.g
> > express(Data,normalize=T, normalize.method="quantiles")
> Normalizing Data
> Background correcting
> Preparing Data
> Error: cannot allocate vector of size 32768 Kb
> In addition: Warning message: 
> Reached total allocation of 500Mb: see help(memory.size)
> 
> I have allocated the maximum for this computer 
> 
> e.g.
> > memory.limit(whatever)
> 
> I have 3 questions that I would be grateful if anyone could help me with:-
> 
> 1. Do all expression calculation and normalisation methods use similar
> amounts of memory (e.g loess?)?

No.

> 
> 2. Does the memory requirement for some methods rise as the chip numbers
> rise?

Yes. (for all methods)

> 
> 3. Reasonably how much memory do I need on a WIN32 to analyse HG133A chips?
> 

It depends on the number of chips. I am not very knowledgeable about 
the behavior of R and the package under Windows. Could you tell more
about the number of chips you have loaded and the total amount of
RAM your computer has ?

> Many Thanks
> Stephen Henderson
> 
> 
> 
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Laurent Gautier			CBS, Building 208, DTU
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