clustermaker2: Different MCL Clustering Results Between Versions

[Aaron Wong]

Hello, 

I was hoping to get your opinion on some confusing results I have been getting using clustermaker2 to cluster a saved Enrichment Map Network. 

I found out that when I use Auto Annotate (which calls on Clustermaker2 for MCL clustering) that clustering results are different between Clustermaker2 v0.9.5 versus v1.1.0. 

Running MCL clustering directly through Clustermaker2 still produces different results between versions under identical settings. The release notes for v1.1.0 do not mention any changes to to MCL algorithm.

Do you have any idea why I may be getting different clustering results?

Aaron 

[Scooter Morris]

Hi Aaron,
    Yes, something changed between clusterMaker 0.9.5 and 0.9.6, but not in the algorithm itself.  I haven't been able to track down exactly the difference, but I think it has to do with some bug fixes in the attribute handling.  My initial thought when I saw this was that the new matrix routines in 1.1.0 were the source of the difference, but I've traced it back to changes that occurred before the switch to the new cluster libraries.  I'll keep working on trying to isolate exactly where the difference came in.

-- scooter

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