[BioC] Hier.Clustering: group size effect

[Kevin R. Coombes]

If you already know the groups, then what's the point of doing 
clustering?  More precisely, what biological question do you think you 
are answering with this method?
	Kevin

Heike Pospisil wrote:
> Hello,
> 
> I have a question concerning hierarchical clustering and the effect of group sizes.
> 
> I would like to select genes that are differentially expressed between group A 
> and group B. Afterwards, I wish to cluster the samples by these genes. In 
> principle, it works fine, but I have a problem if the group sizes are 
> significantly unequal. One example is as e.g.:
> group A: 53 samples
> group B: 12 samples
> The resulting clustering brings group B together, but it is not clearly 
> separated from group A. Then again, if I take 12 samples from group A randomly 
> (to get equal group sizes), the clustering is nearly perfect.
> 
> I use hclust(dist(t(exprs(sub)),method="euclidean"),method="complete") 
> (ncol(sub) = groupA+groupB and nrow(sub) = number of sign.genes) and tried other 
> distance measures, but without improvement.
> 
> Does anybody have a hint which clustering algorithm should be prefered for such 
> unequal group sizes?
> 
> Thanks in advance and best wishes,
> Heike