This is a really basic question but really important to get right! Let's say my two conditions on which I ran differential expression analysis are called A and B. When I summarize the results of decideTestsDGE, it gives me something like this:

        A-B
Down    1310
NotSig  15360
Up      1624

But which of the conditions is considered the baseline when it's calling genes as "down" or "up" regulated? For the comparison between A and B, does "down" mean B is downregulated compared to A, or A is downregulated compared to B?

(On a related note, is there somewhere in the ExactTest output where I can get the actual average value for A and average value for B for each gene, not just the fold-change difference? I would have been able to figure out what "up" or "down" mean if I'd been able to see those.)

The output says that the results are for A-B (i.e., A minus B). That tells you have any gene that is "Up" is higher in A than in B (because the log-expression difference A - B is positive) and any gene that is "Down" is higher in B than in A (because the log-expression difference A - B is negative).

Similarly the sign of the log2-fold-change tells you whether a gene is higher in A or B. A positive logFC means higher in A and a negative logFC means lower in A (i.e., higher in B).

Computing average values for A and B is easy (see for example cpmByGroup) but is not part of the exactTest test or its output.