[BioC] hclust for 13000 genes

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Mar 17 23:11:23 CET 2010


On Wed, Mar 17, 2010 at 5:59 PM, avehna <avhena at gmail.com> wrote:
> 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!.

This error is telling you that you don't have enough RAM to do what
you are trying to do, so to fix this you'll need a way to either get
more RAM or get access to a machine that has more ram.

Maybe you have enough RAM already and you're using R in 32 bit mode?
You didn't tell us the particulars of your machine, so no way to tell


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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