[BioC] How to design matrix on edgeR to study genotype x environmental interaction

[Gordon K Smyth]

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

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