[R] About the breakpoint when making heatmap with lots of variables

[Shi, Tao]

The "breakpoint" you mentioned is irrelevant here.  Clustering 15672 
genes (I assume this is a microarray data) requires lots of memory.  I 
suggest you either filter your gene list down to thousands or just plot 
the column dendrogram without showing the heatmap.

plot(hclust(dist(x)))

...Tao




----- Original Message ----
> From: Meng Wu <mengwu1002 at gmail.com>
> To: r-help at r-project.org
> Sent: Wed, May 19, 2010 7:31:29 PM
> Subject: [R] About the breakpoint when making heatmap with lots of variables
> 
> HI,All

I am trying to create a heatmap with 24 samples with 15672 
> varibles, I read
in the table in R, and then made it as a matrix, then try to 
> create the
heatmap using heatmap(x,...)

However, I received the error 
> message as:
> heatmap(t(x))
Error: cannot allocate vector of size 936.8 
> Mb
R(2925,0xa0b16500) malloc: *** mmap(size=982261760) failed (error 
> code=12)
*** error: can't allocate region
*** set a breakpoint in 
> malloc_error_break to debug
R(2925,0xa0b16500) malloc: *** 
> mmap(size=982261760) failed (error code=12)
*** error: can't allocate 
> region
*** set a breakpoint in malloc_error_break to 
> debug
R(2925,0xa0b16500) malloc: *** mmap(size=982261760) failed (error 
> code=12)
*** error: can't allocate region
*** set a breakpoint in 
> malloc_error_break to debug
R(2925,0xa0b16500) malloc: *** 
> mmap(size=982261760) failed (error code=12)
*** error: can't allocate 
> region
*** set a breakpoint in malloc_error_break to 
> debug
R(2925,0xa0b16500) malloc: *** mmap(size=982261760) failed (error 
> code=12)
*** error: can't allocate region
*** set a breakpoint in 
> malloc_error_break to debug
R(2925,0xa0b16500) malloc: *** 
> mmap(size=982261760) failed (error code=12)
*** error: can't allocate 
> region
*** set a breakpoint in malloc_error_break to 
> debug
R(2925,0xa0b16500) malloc: *** mmap(size=982261760) failed (error 
> code=12)
*** error: can't allocate region
*** set a breakpoint in 
> malloc_error_break to debug


It seems like I do not have enough 
> memory, how can I set a breakpoint 
> as
suggested?

Thanks,

Meng

    
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