Eisen's cluster software implements average linkage clustering by replacing nodes with an average of the leaf nodes represented by the node and by then computing distances from that average. hclust(), on the other hand, uses an average of the distances between all pairs of points in two nodes. Does anyone have any information/opinion as to why one method might be better than the other? Also, does anyone know of any code in R that implements Eisen's algorithm? Thanks. -Ben

Hi, Xcluster does same algorithm as Eisen software. This software can be use within R with ctc package. (Xcluster: http://genetics.stanford.edu/~sherlock/cluster.html) One advantage of this method is that we are not oblige to store the whole distance matrix: Xcluster requires very few memory allocation. A problem could arrive by example when agglomerating 3 points of equal distance (an isometric triangle): * first node will agglomerate two corners with a distance 'd' * second node will agglomerate the last corner with the midle of the other corners with distance 'd'.sqrt(3)/2 Your tree will be difficult to draw as distance are not increasing while agglomerating more and more... but can be easily skip. Antoine Lucas. Le Tue, 29 Nov 2005 13:27:13 -0500 "Wittner, Ben" <wittner.ben at="" mgh.harvard.edu=""> a ?crit: > Eisen's cluster software implements average linkage clustering by replacing > nodes with an average of the leaf nodes represented by the node and by then > computing distances from that average. hclust(), on the other hand, uses an > average of the distances between all pairs of points in two nodes. > > Does anyone have any information/opinion as to why one method might be better > than the other? > > Also, does anyone know of any code in R that implements Eisen's algorithm? > > Thanks. > > -Ben > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Antoine Lucas Centre de g?n?tique Mol?culaire, CNRS 91198 Gif sur Yvette Cedex Tel: (33)1 69 82 38 89 Fax: (33)1 69 82 38 77