Meng Wu
2010-May-20 02:31 UTC
[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]]
Shi, Tao
2010-May-20 16:21 UTC
[R] 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,AllI am trying to create a heatmap with 24 samples with 15672> varibles, I readin the table in R, and then made it as a matrix, then try to> create theheatmap using heatmap(x,...) However, I received the error> message as: > heatmap(t(x))Error: cannot allocate vector of size 936.8> MbR(2925,0xa0b16500) malloc: *** mmap(size=982261760) failed (error> code=12)*** error: can't allocate region *** set a breakpoint in> malloc_error_break to debugR(2925,0xa0b16500) malloc: ***> mmap(size=982261760) failed (error code=12)*** error: can't allocate> region*** set a breakpoint in malloc_error_break to> debugR(2925,0xa0b16500) malloc: *** mmap(size=982261760) failed (error> code=12)*** error: can't allocate region *** set a breakpoint in> malloc_error_break to debugR(2925,0xa0b16500) malloc: ***> mmap(size=982261760) failed (error code=12)*** error: can't allocate> region*** set a breakpoint in malloc_error_break to> debugR(2925,0xa0b16500) malloc: *** mmap(size=982261760) failed (error> code=12)*** error: can't allocate region *** set a breakpoint in> malloc_error_break to debugR(2925,0xa0b16500) malloc: ***> mmap(size=982261760) failed (error code=12)*** error: can't allocate> region*** set a breakpoint in malloc_error_break to> debugR(2925,0xa0b16500) malloc: *** mmap(size=982261760) failed (error> code=12)*** error: can't allocate region *** set a breakpoint in> malloc_error_break to debugIt seems like I do not have enough> memory, how can I set a breakpoint > assuggested? Thanks, Meng> [[alternative HTML version > deleted]]______________________________________________> ymailto="mailto:R-help at r-project.org" > href="mailto:R-help at r-project.org">R-help at r-project.org mailing list> href="https://stat.ethz.ch/mailman/listinfo/r-help" target=_blank > >https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting> guide http://www.R-project.org/posting-guide.htmland provide commented,> minimal, self-contained, reproducible code.