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 Bot?as Talamantes Unidad de Gen?mica Parque Cient?fico de Madrid-UCM Facultad CC Biol?gicas- Planta s?tano 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/

Pedro Bot?as 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 Bot?as Talamantes > Unidad de Gen?mica > Parque Cient?fico de Madrid-UCM > Facultad CC Biol?gicas- Planta s?tano > 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/ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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