[BioC] What is the best way to eliminate non-variants from set of arrays?

[Ruppert Valentino]

Hello,

I am analysing Affymatrix microarray experiment that involve the following 
groups :

Group      No of samples
---------     --------------------

A              4

B              9

C              10

D              2




I would like to get rid of the non-variants to do unsupervised clustering. I 
tried the simple filters like SD and fold change as in the Cluster software 
but I always end up getting some of the technical probes like GAPDH Affy 
coming come up and spoil the cluster. So the question is what is the best 
algorithm to use to eliminate non-variant across the arrays non-specifically 
i.e. without grouping them?

I was thinking of using dChip or eBayes but any suggestion/advice would be 
greatly appreciated as the sample size is small here and the idea is to just 
to eliminate non-variant genes to see if the unsupervised clustering brings 
anything.

Regards

Ruppert