Well, that sort of depends. As it stands right now, if you signed with the agent after the publishing deal was signed, then you don't owe the agent anything. Make sure that you have an addendum to your Agency agreement that excludes this particular deal.
HOWEVER --- If the publisher has only made an OFFER, and you've since signed an agent, I would strongly suggest that you consider allowing the agent to negotiate the offer from the publisher. Yes, you'll have to pay a commission when you otherwise wouldn't have had to, but you'll probably be getting a better deal, since that's what an agent is for.