Dear Luis, Are you asking how to construct a design matrix? Why not design <- modelMatrix(targets, ref="C") as described in the limma User's Guide? Best wishes Gordon > Date: Tue, 15 Mar 2011 14:52:05 -0400 > From: Luis Z <luisgls at="" gmail.com=""> > To: bioconductor at r-project.org > Subject: [BioC] limma design experiment > Message-ID: > > Hi everyone, > > I would like to receive a suggestion on the design model for this > experiment. > > There are 5 different RNA pool families. Each one with three replicates > (Technical?), coming from individuals that receive three different > treatments, a control treatment and T1, T2. The experiment were made : > fam Cy3 Cy5 > slide 1 F1 T1 C > F1 T1 C > .... > F5 T1 C > F1 T2 C > ... > F5 T2 C > > What would you suggest? > > Thanks, > > Luis > -- > Luis Zapata Ortiz > Molecular Biotechnology Engineering > Laboratory of Bioinformatics and Mathematics of the Genome, LBMG. > Center of Mathematical Modeling of the University of Chile. > Av. Blanco Encalada 2120 > 56-2-9784551 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}

Dear Gordon, Thanks, I followed that already. My question is how can i treat each of my family samples as technical replicates and different family as a biological replicate. And if that is what you would suggest. Best, Luis Zapata On Wed, Mar 16, 2011 at 7:39 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote: > Dear Luis, > > Are you asking how to construct a design matrix? Why not > > design <- modelMatrix(targets, ref="C") > > as described in the limma User's Guide? > > Best wishes > Gordon > > Date: Tue, 15 Mar 2011 14:52:05 -0400 >> From: Luis Z <luisgls@gmail.com> >> To: bioconductor@r-project.org >> Subject: [BioC] limma design experiment >> Message-ID: >> >> Hi everyone, >> >> I would like to receive a suggestion on the design model for this >> experiment. >> >> There are 5 different RNA pool families. Each one with three replicates >> (Technical?), coming from individuals that receive three different >> treatments, a control treatment and T1, T2. The experiment were made : >> fam Cy3 Cy5 >> slide 1 F1 T1 C >> F1 T1 C >> .... >> F5 T1 C >> F1 T2 C >> ... >> F5 T2 C >> >> What would you suggest? >> >> Thanks, >> >> Luis >> -- >> Luis Zapata Ortiz >> Molecular Biotechnology Engineering >> Laboratory of Bioinformatics and Mathematics of the Genome, LBMG. >> Center of Mathematical Modeling of the University of Chile. >> Av. Blanco Encalada 2120 >> <56-2-9784551>56-2-9784551 >> > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:20}}