[R] Grouping clusters from dendrograms

[plangfelder]

Hi Julia, 

sorry for the very late reply, your original email was posted while I was on
hiatus from R-help. I'm the author of the dynamicTreeCut package. I
recommend that you try using the "hybrid" method using the cutreeDynamic
function. What you observed is a known problem of the tree method (which, by
the way, was the reason I developed the Hybrid method). 

Using the hybrid method is simple, for example as 

cut2<-cutreeDynamic(dendro,distM = combo2,
maxTreeHeight=1,deepSplit=2,minModuleSize=1)

You can play with the argument deepSplit to obtain finer or coarser modules.

HTH,

Peter 

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