I have a question about the function hclust - Which kinds of distance metrics can be defined, and which kinds of distance metrics correspond to what kind of biological needs? (e.g. I would guess correlation distance would be useful for pathway analysis?) In addition, how can I define it? I read the hclust info in R, and one line states "In this case the dissimilarities between the clusters are the squared Euclidean distances between cluster means. " Is this true for all uses of 'dist'? hc <- hclust(dist(USArrests)^2, "cen") Secondly, in a bioconductor-unrelated question, does anyone know what kind of distance metric is used by Michael Eisen's Cluster? Thank you very much! Regards, Min-han This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient(s) please contact the sender by reply email and destroy all copies of the original message. Thank you. [[alternative HTML version deleted]]