bayesclust?  BHC?
http://www.bioconductor.org/packages/2.11/bioc/vignettes/BHC/inst/doc/bhc.pdf

http://www.biomedcentral.com/1471-2105/10/242 for actual prettypictures

see also https://sites.google.com/site/mdipackage/


On Fri, Oct 12, 2012 at 6:29 AM, Stephen Turner <vustephen@gmail.com> wrote:

> I also was curious if there was another package that assessed
> significance of splits in hierarchical clustering. I've never been a
> big fan of how p-values are expressed on a [0,100] scale on the
> pvclust plots.
>
> Stephen
>
> On Thu, Oct 11, 2012 at 7:05 AM, kh <kh132@le.ac.uk> wrote:
> >
> >  <asl@...> writes:
> >
> > >
> > > I realize questions about packages should go to the package maintainer,
> > > but perhaps I have an old email address (suzuki3_at_is.titech.ac.jp)
> -- no
> > > reply.  Also I have both a general, and a specific, question.
> > >
> > > General question: i've used pvclust before to assess significance of
> > > clusters and obtained reasonable results. However, on a new data set
> (see
> > > below) the results seem odd. I wonder if pvclust is a generally used
> > > package to assess cluster signficance, or if another package/approach
> is
> > > considered standard? The "approximately unbiased" feature of pvclust
> > > compared to regular boostrapping seems attractive.
> > > Specific question: the odd result I am getting concerns a tree with a
> very
> > > clear division into two very distinct top level clusters. However on
> this
> > > data set the subclusters with confidence appear low down in the tree,
> and
> > > the very top most division gets zero significance. I'm suspicious of
> this
> > > given the rather clear top-level clade structure in this data set with
> > > lots of examples and not many NA's, i.e. pretty vanilla data. Also, in
> a
> > > related data set there seems to be a crash: pvclst bootstraps and
> scales
> > > happily for a while, then prints: Bootstrap (r = 1.29)... Done.
> Bootstrap
> > > (r = 1.29)... Done. Error in solve.default(crossprod(X, X/vv)) : Lapack
> > > routine dgesv: system is exactly singular In addition: Warning
> message: In
> > > lsfit(X, zz, 1/vv, intercept = FALSE) : 'X' matrix was collinear
> > > Thank you
> > > Alan`
> > >
> > > _Hi Alan
> > I am getting exactly the same warning message"Error in
> solve.default(crossprod
> > (X, X/vv)) : Lapack routine dgesv: system is exactly singular In
> addition:
> > Warning message: In lsfit(X, zz, 1/vv, intercept = FALSE) : 'X' matrix
> was
> > collinear" and was wondering if you were able to find out why it was
> > happening? Please let me know too
> > Thank you
> > Koirobi.
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> > >
> > >
> >
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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