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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Hello Eleni, as far as I understood and used agnes() the method argument determines only the clustering method. If you use diss=TRUE the distances should be taken from the distance matrix. Birgit Am 28.11.2007 um 12:18 schrieb Eleni Christodoulou:> 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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code.Birgit Lemcke Institut f?r Systematische Botanik Zollikerstrasse 107 CH-8008 Z?rich Switzerland Ph: +41 (0)44 634 8351 birgit.lemcke at systbot.uzh.ch
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
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>