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

	[[alternative HTML version deleted]]

