[BioC] affy & problems with memory

Ettinger, Nicholas nicholas-ettinger at uiowa.edu
Tue Jan 10 20:15:31 CET 2006

Thanks for the tip!

That worked great for GCRMA.  I tried to look but couldn't find anything similar for mas5 or for the LiWong algorithm?

Did I miss something or is the only solution there to get more RAM?


-----Original Message-----
From: Marta Agudo [mailto:martabar at um.es] 
Sent: Tuesday, January 10, 2006 12:36 PM
To: Ettinger, Nicholas; bioconductor-bounces at stat.math.ethz.ch
Subject: RE: [BioC] affy & problems with memory


Marta Agudo PhD
Departamento de Oftalmología
Facultad de Medicina
Campus Espinardo
30100 Murcia- Spain
Phone:+34 968363996

-----Mensaje original-----
De: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] En nombre de Ettinger,
Enviado el: martes, 10 de enero de 2006 17:03
Para: bioconductor at stat.math.ethz.ch
Asunto: [BioC] affy & problems with memory

Hello all!

I have 16 Affy Hg-U133plus2 cel files that I am trying to analyze.  I am
having difficulties generating expression data because of memory
problems.  I am working on a Dell desktop running WinXP.  I can
successfully generate expression values if I use "RMA" but if I try MAS5
or GCRMA or LiWong instead then I consistently get an error message with
"Cannot allocate vector of size 169362 Kb."  To try to increase
available memory I have already done two things:  (a) I right-clicked on
the R icon and changed the box labeled 'Target' to read "C:\Program
Files\R\R-2.2.0\bin\Rgui.exe" --sdi  --max-mem-size=2000M" and (b) I
have increased the virtual memory Total Page File size to 2000MB.  But
it still runs out of memory.

Help! Any suggestions -- I don't really have access to any bigger


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