[BioC] odd results with pvclust

[Stephen Turner]

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 at le.ac.uk> wrote:
>
>  <asl at ...> 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.
> ______________________________________________
> > Bioconductor mailing list
> > Bioconductor at ...
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> >
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor