Hopach cluster quality metrics
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Khan, Anar ▴ 30
Last seen 7.7 years ago
Hi, 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. Thanks, Anar ____________________________ Anar Khan Bioinformatician 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 ====================================================================== = Attention: The information contained in this message and...{{dropped:12}}
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