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 <mengwu1...@gmail.com>
> To: r-help@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
> [[alternative HTML version
> deleted]]
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