Dear Daniela, edgeR can work with any design matrix. Just setup your interaction model using standard R model formula. See for example Chapter 11 of: http://cran.r-project.org/doc/manuals/R-intro.pdf Best wishes Gordon > Date: Mon, 29 Oct 2012 16:24:31 +0100 > From: Daniela Lopes Paim Pinto <d.lopespaimpinto at="" sssup.it=""> > To: bioconductor at r-project.org > Subject: [BioC] How to design matrix on edgeR to study genotype x > environmental interaction > > Dear all, > > I'm currently working with data coming from deep sequencing of 48 small > RNAs libraries and using edgeR to identify DE miRNAs. > I could not figure out how to design my matrix for the following > experimental design: > > I have 2 varieties (genotypes), cultivated in 3 different locations > (environments) and collected in 4 physiological stages. None of them > represent a control treatment. I'm particulary interested on identifying > those miRNAs which modulate their expression dependent on genotypes (G), > environments (E) and G x E interaction. For instance the same variety in > the 3 different locations, both varieties in the same location and both > varieties in the 3 different locations. > > I was wondering if I could use the section 3.3 of edgeR user guide as > reference or if someone could suggest me any other alternative method. > > Thanks in advance > > Daniela ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}