I am having a hard time wrapping my brain around how to structure my results() and if it's even possible.
My design is:
design(dds) = ~ soilmoisture + fungal_tr + soilmoisture:fungal_tr
My understanding for results() is that:
(1) The fungal effect for soilmoisture W (the main effect):
(2) The fungal effect for soilmoisture D; this is, by definition, the main effect (W) plus the interaction term (the extra fungal effect in soilmoisture D compared to soilmoisture W):
The two examples above always compare Fungus 1 to the Sterile Control within W or within D.
However, is it possible to look at the differential expression of Fungus1 between W vs D and still account for the baseline of the sterile control? Or do I have to run DESeq2 like above, and then take the DEG raw counts and rerun DESeq2 to compare the difference between soil moisture?