[R] clustering a sparse dissimilarity matrix

Christian Hennig chrish at stats.ucl.ac.uk
Fri Mar 31 15:31:27 CEST 2006


there are several things unclear with this question.

On Thu, 30 Mar 2006, Giuseppe Pagnoni wrote:

> Dear all,
> I have a BIG dissimilarity matrix (around one thousand by one thousand),
> that I would like to cluster.  Most of the elements of the matrix are
> zero or close to zero.  Is there a way to cluster the matrix
> (hierarchical or partitioning methods) that discards those elements that
> are close to zero (by using a specified threshold on the matrix)?

What do you mean by an "element close to zero"?
An entry in the matrix? Then, what do you mean by "discarding" them? How 
should that help?

> I am
> asking this because otherwise I get a huge amount of clutter for
> singletons or very small clusters.  Also, how can you look for clusters
> of a specified  size, apart from looking visually at the dendrogram?  Is
> there a way to bias the algorithm specifically for clusters of a certain
> size?

What clustering method did you apply and why?
How would you like to specify the size of your clusters (and why)?


*** --- ***
Christian Hennig
University College London, Department of Statistical Science
Gower St., London WC1E 6BT, phone +44 207 679 1698
chrish at stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche

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