[R] pvclust:a general and a specific question

From: <asl_at_tmail.lanl.gov>
Date: Wed, 25 Jun 2008 08:57:52 -0600 (MDT)

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) Also I have both a general, and a specific, question.

  1. General question: i've used pvclust before to assess significance of clusters and got 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.
  2. 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

R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Wed 25 Jun 2008 - 19:13:11 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Wed 25 Jun 2008 - 19:31:50 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive