[BioC] clustering of genes

[Gordon Smyth]

I would like advice about software and appropriate approaches for 
clustering genes.

I have results from a series of 45 cDNA arrays comparing RNA sample 
extracted from a hela human cell line. My collaborators have over-expressed 
a dozen different transcription factor proteins and compared the results 
back to a reference. There are 3-4 replicate arrays for each transcription 
factor. I have classified each gene as likely up, down, neither for each 
transcription factor. Now I would like to do a cluster analysis of the 
genes. I know that there is a long tradition of cluster algorithms for 
microarray results in the cancer context, but I don't have any experience 
with clustering using R.

What software have people found useful for this problem? There are the 
cluster and class packages on CRAN, both of which look promising. Is there 
anything on bioconductor or anything in R specifically directed at 
microarray results?

Many thanks
Gordon
---------------------------------------------------------------------------------------
Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3050, Australia
Tel: (03) 9345 2326, Fax (03) 9347 0852,
Email: smyth at wehi.edu.au, www: http://www.statsci.org