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 [[alternative HTML version deleted]]

Dear Luis, I can't say. Your description of your experiment was too brief for me to follow. Best wishes Gordon > Date: Wed, 16 Mar 2011 18:55:50 -0400 > From: Luis Z <luisgls at="" gmail.com=""> > To: bioconductor at r-project.org > Subject: Re: [BioC] limma design experiment > > 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 at="" 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 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>56-2-9784551 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}