[BioC] hclust and (Eisen+ de Hoon) cluster3 program

Wittner, Ben Wittner.Ben at mgh.harvard.edu
Wed Dec 8 15:27:58 CET 2004

In case this helps, I've not looked at cluster3, but I have looked at the source
code of Eisen's Cluster (i.e., the one for Windows) and I noticed that Cluster's
average agglomeration method seems to compute an average of each cluster (i.e.,
a point whose n-th coordinate is the average of the n-th coordinates of all the
points in the cluster) and then use the distance between those averages whereas
hclust() seems to use the average distance between the points of the two
clusters. In other words, Cluster uses the distance between averages and
hclust() uses the average of distances.

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