[BioC] Hierarchical clustering/distance

[Tan, MinHan]

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
 

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