Denied perhaps? Certainly! (6)
I believe the answer is:
indeed
'certainly' is the definition.
(both can be used to answer in the affirmative)
'denied perhaps?' is the wordplay.
'perhaps?' indicates anagramming the letters (I've seen 'perhaps' mean this).
'denied' with letters rearranged gives 'INDEED'.
(Other definitions for indeed that I've seen before include "Without question" , "Really - what a surprise!" , "Certainly, quite so" , "Certainty" , "Truly or admittedly" .)