Debugging someone's code, I just noticed a slight usability issue with the
results function, which has a '...' argument, so when
results(dds, contrasts=c("group","A","B")) was called, the spelling mistake of the
contrast argument wasn't picked up with a usual 'unused argument' warning, and it defaulted to something the user didn't want. The documentation says that the optional arguments are passed to
filterFun, but that no longer looks to be the case in that filterFun takes a specified set of named arguments.
Not a major thing in the grand scheme of things, but if the apparently unused '...' could be removed, it might lessen the chance of similar user error.