On Fri, Sep 17, 2010 at 1:17 PM, Sunny Srivastava
<research.baba@gmail.com>wrote:

> Dear Dr. Huber,
> Thanks for your reply, but I had looked at this function. What I understood
> from the documentation was: if give the height at which I want to cut, then
> it gives me $upper and $lower, but I guess I have to "hack" to get the
> height which gives me a specific number of clusters?
>
> I am I thinking correctly?
>
>
You could also try the cutree() function.

Sean


> On Fri, Sep 17, 2010 at 10:11 AM, Wolfgang Huber <whuber@embl.de> wrote:
>
> > Sunny
> >
> > the function "cut.dendrogram" from the "stats" package does what you
> want.
> > It's described in the manual page of the "dendrogram" class. Try typing,
> in
> > R:
> >
> >  ? dendrogram
> >
> > Best wishes
> >        Wolfgang
> >
> >
> >
> >
> > On Sep/16/10 12:57 PM, Sunny Srivastava wrote:
> >
> >> Hello Bioconductor Helpers,
> >> I have a question about extracting the clusters of genes after we make
> the
> >> heatmap (say ht4) using the heatmap.2 function. Basically, I want to get
> >> the
> >> clusters which are shown as row dendrogram in the heatmap.
> >>
> >> I understand that ht4$rowDendrogram is an object of dendrogram and it
> >> containes details of all the nodes and branches, but lets say I want to
> >> know
> >> the number of clusters and the genes in each cluster if I terminated the
> >> tree (dendrogram) at a particular height. Also, if I know that I want 12
> >> clusters, how do I know which height I should terminate the tree (or
> >> branching structure)
> >>
> >> I am sorry I am not clear. Please let me know if you need any further
> >> clarifications. Thanks in advance for your help.
> >>
> >> Best Regards,
> >> S.
> >>
> >>
> >> Below is the dump of the matrix *row.scaled.fc2* and the object *ht4*
> >> which
> >> was obtained by using the heatmap.2 function.
> >>
> >>  --
> >
> >
> > Wolfgang Huber
> > EMBL
> > http://www.embl.de/research/units/genome_biology/huber
> >
> >
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