The simplest way I know of, is to recode the factor up front, so that the level you want to use as a reference is the first one.
You could do this with a function like this:
recodeFactor<-function(f, ref=levels(f)[1])
{
lvls<-levels(f)
if(ref== lvls[1]) return(f)
lvls<-c(ref, setdiff(lvls, ref))
f<-factor(as.character(f), levels=lvls)
return(f)
}