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.)