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Rooney is the most obvious worry after getting a nasty kick on his ankle by Chris Brunt at West Brom on Saturday but Evra and Gibson also finished the game moving at less than full tilt and Ferguson will need to be reassured about their fitness before picking any of them.
Nani (hip) might be available, while skipper Nemanja Vidic escaped suspension for his fifth booking of the season, which came one day after the December 31 cut-off point.
Darren Fletcher has warned United should not be sucked in by the belief Stoke are just a team of long-ball merchants. Tony Pulis' in-form Potteries outfit head to Old Trafford trying to prevent their hosts making it a 20-match unbeaten start to the season.
United are one of the few sides they seem incapable of ruffling, having lost all five encounters since their return to the top flight. And the key may be the fact Ferguson's men are not just prepared for an aerial bombardment. They also recognise Stoke can play a bit too.
"Stoke can be physical at times," said the Scotland skipper.
"They put long throws and free-kicks into the box and are willing to go direct. But that is not to neglect the football players they have. Matthew Etherington and Jermaine Pennant like to get at you and dribble.
"Tuncay and Ricardo Fuller are good, attacking-style players who like the ball at their feet too, so they do have options and can cause problems on the ground."
On their past two trips to Old Trafford, Stoke have conceded nine goals, without scoring once. Indeed, a secret weapon in combating Rory Delap's long throws has been established. Without being aware of it, the slope that surrounds the perimeter of Old Trafford prevents Delap launching his bombs in quite the same way, reducing the effectiveness of that particular avenue of Stoke attack.
"Against Stoke, some teams would rather defend the corner than the throw-in," admitted Fletcher.
"But the slope at Old Trafford stops them building up momentum. The pitch is bigger as well so maybe they can't get the throws quite as far into the box.
"It is still a danger but we prepare for it. We do our homework and try to manage it the best way we can."
Stoke defender Robert Huth is available again after suspension. Huth was forced to sit out the victory over Everton at the Britannia Stadium on Saturday. Fuller is looking to retain his place up front alongside Kenwyne Jones ahead of Jon Walters.
Jones is determined to enjoy his football and put his personal worries to one side. According to Stoke manager Pulis, the striker is trying to cope with a family tragedy which he believes affected his performances in recent weeks. Jones responded with his first goal in six games in the victory against Everton.
In an interview on the club website, Jones said: "When it comes to football it does tend to take your mind off stuff. Problems are part of life and sometimes it does tend to spill over into football.
"In football you have to enjoy every day that you have because when its finished, that's it."
It was Jones' seventh goal for the club following his £8million arrival from Sunderland in August.
"In the past weeks, chances have been few so it was good to be off the mark again, " he said.
"It was a great way to start the new year. "Things are going well and we are looking forward to going there (to Old Trafford) and doing our best."
Pulis was delighted to see Jones end his duck with a powerful first-half header to put Stoke in front. The striker's flick-on was then turned into his own net by Phil Jagielka for the second goal.
Pulis told the Stoke Sentinel: "There had been a few moans and groans, but you get that at most grounds. But the fans were brilliant with him in this game, and I am so pleased for him.
"He has had an issue off the field that might have affected him a bit, but we haven't put any pressure on him. We have let him deal with it himself.
"I was very pleased when he scored the goal. That gave him the confidence to play as well as he did."
And Pulis is convinced there is more to come from his seven-goal top scorer. He added: "Although Kenwyne's performances maybe dipped a little bit, we have great belief in him."