Lee has added 12 new players to the Reebok Stadium squad after replacing Allardyce at the helm towards the end of last season.
"We have made a lot of changes and most of the players have had five to six weeks to work together," said Lee, who added former Portsmouth defender Andy O'Brien to his squad on Monday.
"But it may take time to get things the way I want and I hope people are patient.
"That is not to excuse the performance against Newcastle as we just did not turn up in the first half.
"I am now aiming for a response at Fulham (on Wednesday).
"They will be looking to get at us as it is their first home game but we have to cope with that."