About the breakpoint when making heatmap with lots of variables

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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