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@kh-5548
Last seen 9.6 years ago
<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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