[BioC] clustering of genes

[w.huber at dkfz-heidelberg.de]

Hi Gordon,

here some methods that I have sometimes found useful for visualization:

- the function heatmap() in package:mva (together with
package:RColorBrewer and package:geneplotter::colorRamp)
- Correspondence Analysis - package:MASS::corresp
- Multidimensional Scaling - package::mva::cmdscale

I am not aware of universally optimal recommendations on which metric or
variable scaling to use, so you'll probably need to try.

For clustering the TFs, the class discovery package "isis" by Anja von
Heydebreck could be useful [1].

And rather than completely unsupervised clustering, it may also be
fruitful to define a "query profiles" and then look for genes that are
close to these. Useful query profiles could be ones that are only "up" for
a single TF, or for a pair of TFs, etc.

Best  -

  Wolfgang


[1] http://www.molgen.mpg.de/~heydebre/software.html

-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/mga/whuber
-------------------------------------

On Fri, 16 May 2003, Gordon Smyth wrote:

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