[BioC]: Clustering with Diana

Jenny Bryan jenny at stat.ubc.ca
Thu Dec 16 20:59:00 CET 2004

I recommend that you start with the documentation and examples for the
'heatmap' function.  This creates heatmaps of your underlying data,
augmented by optional dendrogram representations of clusterings of
your rows (could be genes) and columns (could be arrays).  In its
default mode, it performs the clustering for you and it will do
agglomerative hierarchical, I believe.  Start there and get

Then, you can do something more advanced -- namely, request a
non-default clustering method.  You maybe able to do this using the
'hclustfun' argument of 'heatmap' (i.e. specify 'diana' here) or you
could perform your clustering in advance, using 'diana' if you like,
and pass those results as dendrograms to 'heatmap'.

Can't help you with Treeview.

Good luck, Jenny

Anthony Bosco writes:
 > Hi,
 > could someone please help with Diana clustering and visualisation.
 > I would like to do 1-way (genes only) and 2-way (genes and samples) 
 > clustering and visualise as a heatmap or in Treeview software.
 > regards
 > Anthony
 > -- 
 > ______________________________________________
 > Anthony Bosco - PhD Student
 > Institute for Child Health Research
 > (Company Limited by Guarantee ACN 009 278 755)
 > Subiaco, Western Australia, 6008
 > Ph 61 8 9489  , Fax 61 8 9489 7700
 > email anthonyb at ichr.uwa.edu.au

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