**0**wrote:

Hi, I am doing hierarchical clustering on TCGA data from several tissues. I perform the hierarchical clustering several times, based on different omics data, and would like to choose the best hierarchical clustering. I am looking for a hierarchical equivalent to looking at cluster homogeneity / separation / silhouette score that is used when evaluating non-hierarchical clustering solutions. Is anyone familiar with such generalizatoin of homogeneity / separation / silhouette score to tree structures?

**59k**• written 2.4 years ago by nimrodrap •

**0**

Try apcluster, I can almost promise to you that no matter the data, it will give you the best results. I'm quite surprised that it hasn't become de facto standard in all things bioinfo..

8.7kThanks, but this is a clustering algorithm. I am looking for ways to evaluate a given hierarchical clustering. I don't see that apcluster has any such evaluation.

0how about rand indexing for each cluster(ing) and then comparing the scores? implemented in clusteval R package.

13k