Be very careful on how you handle the deposit. You cannot set the rent arrear off straight away. If it is a assured shot hold tenancy agreement and you failed to put the deposit in protection within time limit you are at risk of penalty.
Therefore the best thing to do is to return the deposit you hold to the tenant, making sure there is witness for the act and written confirmation that you have returned the deposit. Then if the tenant and you both agree, he can hand the money back to you as rent.