Hi,

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.

Best,

Jean Elbers

hi Jean,

Thanks for the question, this wasn't explicitly stated in the documentation, so I've updated it, here are the new sections in man pages and vignette:

https://github.com/mikelove/fishpond/commit/87639eafb3301ec4cc5c91f6dce3fdfb8632d300