I noticed that the order of factors in
swish(x="condition") analysis makes a difference in the sign of the log2fc values. My question is which factor level is the reference if for example one has two factors in the order
MUTANT, WT for
condition. My assumption is
WT is actually the reference level so a positive log2fc indicates up-regulation relative to
MUTANT and a negative log2fc indicates down-regulation. But it could also be the other way around.