[BioC] odd results with pvclust

[kh]

 <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.
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