From: Weiwei Shi <helprhelp_at_gmail.com>

Date: Thu 19 Oct 2006 - 00:04:59 GMT

Date: Thu 19 Oct 2006 - 00:04:59 GMT

Dear Chris:

I tried to use cor+1 but it still gives me sil width < 0 for average.

On 10/18/06, Weiwei Shi <helprhelp@gmail.com> wrote:

> Dear Chris:

*>
**> thanks for the prompt reply!
**>
**> You are right, dist from pearson has negatives there, which I should
**> use cor+1 in my case (since negatively correlated genes should be
**> considered farthest). Thanks.
**>
**> as to the ?cluster.stats, I double-checked it and I found I need to
**> restart my JGR, until then the help page function starts to accept
**> newly loaded package, like fpc for this case.
**>
**> sorry for the confusion,
**>
**> weiwei
**>
**> On 10/18/06, Christian Hennig <chrish@stats.ucl.ac.uk> wrote:
**> > Dear Weiwei,
**> >
**> > > btw, ?cluster.stats does not work on my Mac machine.
**> > >> version
**> > > _
**> > > platform i386-apple-darwin8.6.1
**> > > arch i386
**> > > os darwin8.6.1
**> > > system i386, darwin8.6.1
**> > > status
**> > > major 2
**> > > minor 3.1
**> > > year 2006
**> > > month 06
**> > > day 01
**> > > svn rev 38247
**> > > language R
**> > > version.string Version 2.3.1 (2006-06-01)
**> >
**> > Because I don't have access to a Mac, I can't tell you anything about
**> > this, unfortunately.
**> > I always thought that my package should work on all platforms if it passes
**> > all the standard tests for packages?
**> > (Is there anyone else who could comment on this please?)
**> >
**> > > I have a sample like this
**> > >> dim(dd.df)
**> > > [1] 142 28
**> > >
**> > > and I want to cluster rows;
**> > > first of all, I followed the examples for cluster.stats() by
**> > > d.dd <- dist(dd.df) # use Euclidean
**> > > d.4 <- cutree(hclust(d.dd), 4) # 4 clusters I tried
**> > > cluster.stats(d.dd, d.4) # gives me some results like this:
**> > >
**> > > $cluster.size
**> > > [1] 133 5 2 2
**> > >
**> > > $avg.silwidth
**> > > [1] 0.9857916
**> > >
**> > > but when I tried to use pearson dist here, by visualization, i think 4
**> > > or 5 clusters are good for pearson dist, but it gave me a very bad
**> > > avg.siqlwidth
**> > >
**> > > d.dd <- as.dist(cor(t(x),method="pearson")) # is This correct?
**> > > $cluster.size
**> > > [1] 86 31 6 19
**> > >
**> > > $avg.silwidth
**> > > [1] -0.09543089
**> >
**> > cor can give negative values, which doesn't fit the usual definition
**> > of a distance. I don't know what as.dist does in this case, but I think
**> > that, depending on your application, you should rather use the absolute
**> > value of the correlation, or 1+cor.
**> >
**> > > btw, what's $seperation? where can I find the detailed explanation on
**> > > the output from cluster.stats?
**> >
**> > This is documented on the cluster.stats help page:
**> >
**> > separation: vector of clusterwise minimum distances of a point in the
**> > cluster to a point of another cluster.
**> >
**> > Best regards,
**> > Christian
**> >
**> >
**> > *** --- ***
**> > Christian Hennig
**> > University College London, Department of Statistical Science
**> > Gower St., London WC1E 6BT, phone +44 207 679 1698
**> > chrish@stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche
**> >
**>
**>
**> --
**> Weiwei Shi, Ph.D
**> Research Scientist
**> GeneGO, Inc.
**>
**> "Did you always know?"
**> "No, I did not. But I believed..."
**> ---Matrix III
**>
*

-- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III ______________________________________________ R-help@stat.math.ethz.ch 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 Thu Oct 19 20:30:02 2006

Archive maintained by Robert King, hosted by
the discipline of
statistics at the
University of Newcastle,
Australia.

Archive generated by hypermail 2.1.8, at Thu 19 Oct 2006 - 11:30:13 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.
*