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]]