I would like some advice on RNA-seq analysis. I have three groups (control, mutant 1 and mutant 2). we would like perform a one-way anova/GLM and to analyse all three groups pair wise. So analyse all three groups to test for significance, then esablish if any gene is changed bewteenany of the groups: control vs mutant 1; control vs mutant 2; mutant 1 vs mutant 2. However, we are running into problems.
Is it possible to do this in DESeq2 or EdgeR, or should iuse Genespring or Partek?