So I realized I had to convert my dd.daisy to a matrix and used:
ddmatrix.daisy<-as.matrix(dd.daisy)
and then I passed that in as the distM:
> cutreeDynamic(as.hclust(dd.diana), cutHeight = NULL, minClusterSize = 2,
method = "hybrid", distM = ddmatrix.daisy,deepSplit =
(ifelse(method=="hybrid", 1, FALSE)),maxCoreScatter = NULL, minGap = NULL,
maxAbsCoreScatter = NULL, minAbsGap = NULL,useMedoids = FALSE,
maxDistToLabel = cutHeight,respectSmallClusters = TRUE, verbose = 2, indent
= 0)

However, now I am getting a different error:

 Detecting clusters...
..cutHeight not given, setting it to 0.847  ===>  99% of the (truncated)
height range in dendro.
Error in ifelse(method == "hybrid", 1, FALSE) : object 'method' not found

Anny suggestions on how to fix this?

Joanna

	[[alternative HTML version deleted]]

