[BioC] gcrma on small computers

Phguardiol at aol.com Phguardiol at aol.com
Thu Jan 15 16:37:49 MET 2004

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 ! 


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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