[BioC] Affymetrix analysis with two replicates

[James W. MacDonald]

Pedro Botías wrote:
> 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

I would recommend the limma package. See the User's Guide which contains 
a huge amount of useful information, in particular the section covering 
2X2 factorial designs using Affy chips.

HTH,

Jim

> 
> *********************************
> 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/
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623