I am using DESeq to perform differential expression analysis. I have read and followed the instructions in the user manuals. I am calling differential expression, using this type of command: res = nbinomTest( cds, "untreated", "treated" ). I am assuming that untreated will be assigned as condition A, and that will correspond to BaseMean A in the output. I would like to make sure that the first condition written in the command will always be assigned to condition A, regardless of other factors such as alphabetical order, for example. Thank you.