[R] Affymetrix data analysis

[Sicotte, Hugues Ph.D.]

Tristan, 
I have a soft spot for problems analyzing microarrays with R..

for the memory issue, there have been previous posts to this list..
But here is the answer I gave a few weeks ago.
If you need more memory, you have to move to linux or recompile R for
windows yourself..
.. But you'll still need a computer with more memory.
The long term solution, which we are implementing, is to rewrite the
normalization code so it doesn't
Need to load all those arrays at once.

-- cut previous part of message--
The defaults in R is to play nice and limit your allocation to half
the available RAM. Make sure you have a lot of disk swap space (at least
1G with 2G of RAM) and you can set your memory limit to 2G for R.

See help(memory.size)  and use the memory.limit function


Hugues 


P.s. Someone let me use their 16Gig of RAM linux
And I was able to run R-64 bits with "top" showing 6Gigs of RAM
allocated (with suitable --max-mem-size command line parameters at
startup for R). 
 

-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Benilton Carvalho
Sent: Thursday, February 01, 2007 6:47 PM
To: Tristan Coram
Cc: R-help at stat.math.ethz.ch
Subject: Re: [R] Affymetrix data analysis

The bioconductor mailing list is probably a better place to ask this  
type of question.

bioconductor at stat.math.ethz.ch

But we also need to know what arrays are you working with, what the  
errors are, what your sessionInfo() is....

Let us know, ok?

b

On Feb 1, 2007, at 5:46 PM, Tristan Coram wrote:

> Hi,
>
>
>
> I am trying to read in my Affymetrix CEL files (48 files, total  
> ~600 MB) but
> I keep getting memory errors.  Can somebody please help me with  
> this.  Or is
> therea remote server I can send my data to for computation?
>
>
>
> Any help is much appreciated.
>
>
>
> Thanks
>
>
>
>
>
> Dr. Tristan Coram
>
> Postdoctoral Research Associate
>
> Research Plant Pathologist/Geneticist
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>
>
> United States Department of Agriculture
>
> Agricultural Research Service
>
> Wheat Genetics, Quality Physiology & Disease Research
>
>
>
> 209 Johnson Hall
>
> Washington State University
>
> Pullman, WA 99163
>
>
>
> Office: +1 509 335-1596  Fax: +1 509 335-2553
>
> Email: tcoram at mail.wsu.edu
>
>
>
>
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