Thank you, Peter.
This worked.
I appreciate your time and help.

Regards,
Joanna

On Wed, Feb 27, 2013 at 1:21 AM, Peter Langfelder <
peter.langfelder@gmail.com> wrote:

> On Tue, Feb 26, 2013 at 8:34 AM, Joanna Papakonstantinou
> <joanna.papa@gmail.com> wrote:
> > 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?
>
> Yes, leave out the 'deepSplit = (ifelse(method=="hybrid", 1, FALSE))'
> from the call. This is not really a cutreeDynamic problem, it is a
> perhaps somewhat confusing aspect of R language. If you don't specify
> deepSplit, its default value will be evaluated within the function
> 'interior' where the variable 'method' is defined. If you do specify
> deepSplit, the expression that you specify is evaluated from 'outside'
> the function where the variable 'method' is undefined. Thus, the
> seemingly same expression can lead to two different results.
>
> In fact, you may want to leave out all arguments for which you are
> using a default value, it will make your call shorter and less prone
> to the type of error you just experienced.
>
> HTH,
>
> Peter
>



-- 
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*Joanna Papakonstantinou, Ph.D.*

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