[BioC] gcrma on small computers

Zhijin Wu zwu at jhsph.edu
Thu Jan 15 21:55:33 MET 2004

We are about to release a new version of GCRMA which has an option
"fast" that takes much less memory, faster and gives almost identical
result to the full version. 
  Please let me know if you would like the test version.


Zhijin(Jean) Wu

On Thu, 15 Jan 2004 Phguardiol at aol.com wrote:

> Hi all
> this is just a short info for users limited by 32 bits PC who d like to use gcrma:
> here is my configuration:
> OS: Win XP Pro
> CPU Xeon 2.40 GHz
> RAM 3.62 Go
> R 1.9dev Jan 12, 2004
> Affy 1.4.9 - Gcrma 1.0.1 - Biobase 1.4.2 - reposTools 1.3.12 - tkWidgets 1.3.14 (all the last dev packages downloaded on monday)
> parameter for R properties: "C:\Program Files\R\rw1090dev\bin\Rgui.exe" --max-mem-size=3500M
> this last line is crucial ! 
> With these I ve been able to run 25 U133A Affy chips and it took me something like 20-30 minutes. The max memory that was used was ~ 1.2 Go. 
> With the previous R.1.8.1 and the corresponding packages it was not possible to finish the same run because of memory limitation.
> I m planning to run ~ twice this number of U133A chips soon and will let you know what I can obtain with this. Hope it helps some users ! 
> Philippe
> Is there a project of developing a sort of RMAexpress for GCRMA which would allow us to run more chips with regular 32 bit systems ?
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