MCL Cluster results panel

[ZP]

HI sorry to ask such a basic question, but having used MCL cluster  to seperate clusters, the results panel delinates the clusters, but also offers a score. what exactly does the score represent? the cluster coefficient? what constitutes a "good" versus a "bad" score?

thanks

ZP

[Scooter Morris]

Hi,
    Currently, if the algorithm itself does not provide a score, clusterMaker2 (which I assume you are referring to) uses a simple modularity calculation, that's defined for each cluster as:
    modularity = (innerEdges/edgeCount) - ((2*innerEdges - outerEdges)/(2*edgeCount))²

So, in general, a high modularity (more inner edges than outer edges) is good.   Recent papers have suggested that Silhouette might be a better measure, so I'll probably be looking to move to that at some point in the future.

-- scooter

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[Zudin Puthucheary]

Thank you!

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