[BioC] Hopach cluster quality metrics

Khan, Anar Anar.Khan at agresearch.co.nz
Tue Oct 14 23:39:23 CEST 2008


Is it possible to obtain a quality metric indicating the "tightness" of
each cluster generated by the hopach package? - e.g the silhouette
averaged across all cluster elements; or the distance averaged over all
pairs of cluster elements. makeTree appears to calculate an average
distance for each node in the dendrogram (these values are displayed by
the MapleTree viewer), but the return value of makeTree refers to nodes
using arbitrary IDs, and mapping these back to cluster labels is beyond
me. I would like to obtain a text dump of cluster labels and
corresponding cluster quality metrics, if possible.


Anar Khan
T +64 3 489 9154
E anar.khan at agresearch.co.nz

AgResearch Limited
Invermay Agricultural Centre
Puddle Alley, Private Bag 50034, Mosgiel, New Zealand
T  +64 3 489 3809   F  +64 3 489 3739  www.agresearch.co.nz

Farming Food and Health. First
Te Ahuwhenua Te Kai me te Whai Ora. Tuatahi

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