I am trying to understand the directionality of the log2 fold change that is reported by DESeq2.
I see in the manual that it says that the first level of the factor will be taken as the dominator for calculations by DESeq2. I also see that the order of the factor levels matters when results() is called. Can you elaborate on how those two work together. For example, lets suppose I am testing between level A and level B, would the results be wrong if in the DESeq() call level A was first, but in the results() call level B was first?