[BioC] odd results with pvclust

[asl at tmail.lanl.gov]

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`