From cireeric at alumni.rice.edu  Tue Jul 19 06:34:38 2005
From: cireeric at alumni.rice.edu (cireeric@alumni.rice.edu)
Date: Tue, 19 Jul 2005 06:34:38 +0200 (CEST)
Subject: [Rd] mac os x crashes with bioconductor microarray code (PR#8013)
Message-ID: <20050719043438.A2510A22C@slim.kubism.ku.dk>

Full_Name: Eric Libby
Version: 2.1.1
OS: OS Tiger
Submission from: (NULL) (65.93.158.117)


I am trying to analyze microarray data of 42 human arrays. I typed in the
following instructions:
library(affy)
Data <-ReadAffy()
eset <- expresso(Data, normalize.method="invariantset", bg.correct=FALSE,
pmcorrect.method="pmonly",summary.method="liwong") 

And I get some sort of memory error that crashes the R program. Specifically it
states:
R(1763) malloc: *** vm_allocate(size=346857472) failed (error code=3)
R(1763) malloc: *** error: can't allocate region
R(1763) malloc: *** set a breakpoint in szone_error to debug
R(1763) malloc: *** vm_allocate(size=346857472) failed (error code=3)
R(1763) malloc: *** error: can't allocate region
R(1763) malloc: *** set a breakpoint in szone_error to debug
Error: cannot allocate vector of size 338724 Kb
R(1763) malloc: *** vm_allocate(size=8421376) failed (error code=3)
R(1763) malloc: *** error: can't allocate region
R(1763) malloc: *** set a breakpoint in szone_error to debug


Any ideas? My computer has 2gb of RAM and 100 gb free. I would think that
analyzing 42 microarrays would not be too difficult. Thanks,
Eric



[Rd] mac os x crashes with bioconductor microarray code (PR#8013)
cireeric@alumni.rice.edu