[BioC] hclust for 13000 genes

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Wed Mar 17 23:09:11 CET 2010

The first answers is that you need to make sure you computer has enough memory, and that R can access that memory.  See memory.size() and memory.limit() for answers.

The second answer is: are you *sure* you want to cluster 13,777 genes?  That's an awful lot to visualise and interpret.....
From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of avehna [avhena at gmail.com]
Sent: 17 March 2010 21:59
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] hclust for 13000 genes

Hi There:

I'm trying to cluster 13777 genes that are differentially expressed across
three different treatments but I'm getting the following error:

R(32949) malloc: *** mmap(size=1518448640) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Error: cannot allocate vector of size 1.4 Gb
Execution halted

I wonder how could I fix it in order to get the clusters and the heatmap
with the expression profile. I would appreciate any suggestion from you!.

Thank you so much for your help in advance,


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