Eleni,
The method= argument is in reference to how clusters are
constructed, not how the dissimilarity or distance is calculated. If
you pass agnes diss=TRUE then it will use the distances you have
calculated by whatever means. method="complete" means that clusters are
evaluated by the maximum distance of a candidate sample to the set of
samples in the cluster, rather than the average. Yo can find
descriptions of these algorithms in most any text on clustering.
Dave Roberts
Eleni Christodoulou wrote:
> Hello all!
>
> I am performingsome clustering analysis on microarray data using
> agnes{cluster} and I have created my own dissimilarity matrix according to a
> distance measure different from "euclidean" or "manhattan" etc. My question
> is, if I choose for example method="complete", how are the distances
> between the elements calculated? Are they taken form the dissimilarity
> matrix I have provided as the first argument?
> clust.complete.agnes<-agnes(as.dist(D),diss="TRUE",method="complete")
>
>
> Thank you very much,
> Eleni
>
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>
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