[BioC] U133plus2.0 memory problem

James W. MacDonald jmacdon at med.umich.edu
Wed Apr 27 15:02:18 CEST 2005

kfbargad at lg.ehu.es wrote:
> Sorry this has come up many times and I have looked for an answer in 
> the mail archives, but I couldn´t find anything regarding amount of 
> memory for many U133plus arrays.
> I have 60 U133plus2.0 arrays and I wanted to do some NUSE plots, but I 
> can´t even read in the arrays using ReadAffy() and I know fitPLM() is 
> more demanding.
> I am running R 2.0.1 and affy 1.5 on a Pentium 4 with Windows 2000 OS, 
> 1G RAM. I tried increasing the memory by
> memory.limit(700000) 

You should append --max-mem-size=1000M to the target field of the 
shortcut you use to start R. This will still not allow you to read in 
and process 60 of the 133plus2 chips. I have 2 Gb and I bet I would have 
trouble with that many chips. You will likely need to increase the RAM 
in your computer, and would probably be better off using Linux, as the 
memory management appears to be much better on that OS.

Note you don't have to install Linux on your comp; you can use Quantian 
which boots Linux off a CD and has R and BioC available.

If all you need are expression values, look at ?justRMA which will be 
able to process all 60 chips with only 1 Gb RAM.



> but still get the error "cannot allocate vector of size 635107
> any suggestions??
> thanks,
> David
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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