[BioC] Affymetrix analysis with two replicates

[Pedro Botías]

Hello,

I need to analyze an experiment with the following design:
- Mutant vs WT
- WT-treatment vs WT
- Mutant-treatment vs Mutant

We have 2 replicates of each experiment or chip.
What method is the appropriate one to carry out this analysis type?. We have
carried out the analysis by means of software of Affymetrix but we wanted to
prove other tools to compare results
Thank you

*********************************
Pedro Botías Talamantes
Unidad de Genómica
Parque Científico de Madrid-UCM
Facultad CC Biológicas- Planta sótano
Universidad Complutense de Madrid
28040 Madrid
Tel: 91 3945036
FAX 91 3944883
e-mail: pbotias at bio.ucm.es
Web: http://www.ucm.es/info/gyp/genomica/