[BioC] interaction analysis

[phguardiol at aol.com]

Dear R users

I would like to have your opinion about the way (and the package that 
would be able to run this issue) to analyse gene expression data 
"around transcription factors":
there are biological situations in which multiple factors 
(Transcription factors TF or other cofactors) are involved in the fact 
that a gene is transcribed, in a way that if TF1 is expressed but not 
TF2, gene3 is lowly expressed, same if TF2 alone is expressed, and it 
is only when both TF1 & TF2 are expressed that gene3 is highly 
expressed. This leads me to think about synergy between TF / 
interaction term.
I d like to explore this in a model we work on in our lab using GEX 
chips. I was thinking of creating a new variable that would be TF1 
signal intensity x TF2 signal intensity and see which gene transcripts 
correlate with this product term. What is your opinion about such an 
approach ? Is there a package that would allow me to run this, given 
the fact that I would like to study all 2x2 interaction terms with the 
whole set of TF identified on our HT12 illumina chips.

As anyone being doing this kind of analysis ? If so should I consider 
using raw signal of log transformed product term ?

Hoping to be not too confused

Best wishes for 2009

Regards

Philippe Guardiola