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