I have the following setup for my rna-seq experiment:
5 samples Control 5 samples 1x concentration of chemical compound 5 samples 10x concentration of chemical compound
My workflow is Hisat2 > Stringtie > ballgown
Now, for ballgown "stattest", how would you test considering my experimental setup. I would just do two tests "control vs 1x" and "control vs 10x". But I guess to analyse all three conditions in one statistical test would be better. Is there a way to do this using ballgown?