[BioC] Memory problem with RMA

[James MacDonald]

You probably need to add --max-mem-size=1G after RGui.exe in the target
field of your R shortcut.

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> <Phguardiol at aol.com> 08/09/03 06:46AM >>>
Hi,
I d like to compare results obtained with different approaches with a
set of 
9 HU133A chips. One of these would be to use the rma background
correction 
method and the invariant set normalization method but it seems that
with ONLY 9 
chips I am running out of memory !!! I have 1 Go RAM on XP Pro R1.7.1
and RMA 
1.3.6... and nothing is running aside this program. I was expecting it
to run 
under these conditions !!! Philippe
>  library(affy)
> data<- ReadAffy()
> data2<-expresso(data, bgcorrect.method="rma", 
normalize.method="invariantset", pmcorrect.method="pmonly",
summary.method="medianpolish")
background correction: rma 
normalization: invariantset 
PM/MM correction : pmonly 
expression values: medianpolish 
background correcting...Error: cannot allocate vector of size 35644 Kb
 

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