[BioC] HEATMAP on LARGE DATA

[Antoine Lucas]

Hi,

For large data sets, hcluster will requires twice less memory than hclust (package amap).

For even larger data sets, you can use xcluster program from Gavin Sherlock
http://genetics. stanford.edu/~sherlock/cluster.html

Package ctc has all tools dialog with this [free] software.

And for visualization, I recommend TreeView or Freeview
http://magix.fri.uni-lj.si/freeview

But exploration on very large tree should be analysed carefully as each branch could be switch with another one like that:

--- A  == --- A
 +- B      +- C
  + C       + B

Regards,

	Antoine Lucas.



Le Mon, 13 Mar 2006 22:22:53 -0500
Sean Davis <sdavis2 at mail.nih.gov> a écrit:

> 
> 
> 
> On 3/13/06 21:08, "mark salsburg" <mark.salsburg at gmail.com> wrote:
> 
> > I am having trouble getting the function heatmap() to work on the following
> > gene expression
> > 
> >> dim(SAMPLES_log)
> > [1] 12626    20
> > 
> > 
> >            sample1 sample2...................sample20
> > gen1
> > gen2
> > gen3
> > ....
> > gen12626
> > 
> > 
> > 
> > I have converted SAMPLES_log to a numeric matrix using:
> > 
> > as.matrix(SAMPLES_log)
> > 
> > when I use the following command:
> > 
> > heatmap(SAMPLES_log)
> > 
> > Error: cannot allocate vector of size 622668 Kb
> > In addition: Warning messages:
> > 1: Reached total allocation of 1022Mb: see help(memory.size)
> > 2: Reached total allocation of 1022Mb: see help(memory.size)
> 
> Mark,
> 
> In order to do a heatmap on 12000 genes, a triangular matrix of size
> 12000x12000/2 needs to be calculated.  This is large and will often result
> in the out-of-memory error that you see.  I don't often find that clustering
> that many genes is meaningful in any major way, particularly since you will
> be including a large number of genes that do not vary in the samples.  If
> you really need to do this, I would suggest that you use an external program
> like cluster/treeview, as they may be somewhat less memory-hungry than R
> (but I haven't tested that directly).
> 
> > Is there some library in BioConductor that will allow me to output a
> > heatmap. I want to compare the expression of the first 10 samples with the
> > last 10 samples.
> 
> If you want to do an unsupervised clustering of samples, use just hclust.
> 
> If you want to do an unsupervised clustering of samples AND genes, I would
> suggest reducing the number of genes using a filter for genes that show
> variability (by using, say, the top 500 genes when sorted by coefficient of
> variation, for example).  In other words, there is no need to include a gene
> in a heatmap that is the same for all samples.
> 
> Ultimately, though, if you want to compare gene expression in two groups of
> samples, you are asking a question that is best answered using a supervised
> method, like a t-test.  There are numerous ways to do a t-test between two
> groups including the limma, siggenes, and multtest packages.
> 
> Hope that helps.
> 
> Sean
> 
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-- 
Antoine Lucas
Centre de génétique Moléculaire, CNRS
91198 Gif sur Yvette Cedex
Tel: (33)1 69 82 38 89
Fax: (33)1 69 82 38 77