Hello!
I am using your (great) platform to analyze a RNAseq dataset, in which I have two discrete variable, treatment and sex, and I was hoping to make some graphs, but when analysing with the nested model, it looks like I can only choose to put the control first (“control_Male vs treated_Male” vs “control_female vs treated_Female”) and I the rest of my data is rather puting the treatment first, so the log FC shown the differential expression from the control rather than the opposite. Is there any way to make it so the disply would show differential expression of the treatment with control as the reference in the nested model?
Thank you very much for this great tool!