Wayne Rooney is a major doubt for Manchester United's trip to Queens Park Rangers on Saturday, with the striker's match fitness for the Champions League last-16 second leg with Real Madrid now a concern for Sir Alex Ferguson.

The manager said: "He came in yesterday [Wednesday] for the first time. The medical people are dealing with him. It's just a bad sinus infection. He got it on Saturday morning and since then he's been on medicines. But he came in on Wednesday and hopefully he'll start training on Thursday. I wouldn't think he's in contention for Saturday."

Rooney missed Monday night's 2-1 FA Cup fifth-round win over Reading at Old Trafford and, if he does miss the match at QPR, his next potential game would be Norwich City's visit on Saturday week. By then it would be two and a half weeks since Rooney played competitively – in the 1-1 draw at Real on 13 February.

Rooney and Ferguson each accept he requires regular games to keep his match sharpness, so the manager would be concerned about how fit the Liverpudlian would be to start the return leg against José Mourinho's side on 5 March.

Ferguson faces a fight to keep Nani at the club as the winger's contract is due to expire in summer 2014 and he wants a guaranteed place or may move on. If so, United would be likely to sell him at the close of this season to ensure he does not leave the following summer for free. "Definitely we want to keep him," Ferguson said. "He's one of the best match-winners in the game – and I'm including the whole of Europe. He showed that again on Monday night [in the win over Reading]. Now he's back, fit and training well, he's a consideration." There's no doubt about that. It gives me a headache because [Antonio] Valencia has been a fantastic player for us. He's [Nani] capable of scoring the most incredible goals. Look at his goal against Everton last year, he dinked the goalkeeper after playing two one-twos: magnificent.

"David [Gill, the chief executive] has been speaking to his agent for quite a few weeks now. It's up to the boy himself. He's got a year and a half left, I would prefer to keep him to the end of his contract. But I think he wants guaranteed first team football."

Ferguson's side are 12 points ahead of Manchester City and he dismissed Roberto Mancini's claims that United will allow them back into the title race by failing to win all of their remaining 12 games.

"I can understand from City's point of view that they keep going on about: 'If we [United] drop points,'" he said. "But the fact of the matter is they will drop points, too; that's for sure. That's where we are. In the run-in you expect to drop a few points but so will they. To be honest, it's always a hard run-in in the Premier League. With the right attitude and the right players, we have a chance [of winning the title]."

While Phil Jones is ruled out of the trip to QPR and faces a fight to be fit to face Madrid due to his ankle injury – he has an "outside chance", the manager said – Paul Scholes should return soon. "He's got a little knee injury," said Ferguson. "We've sent him to a specialist. There's probably something floating in the knee, which he's had many years. He'll be back, absolutely. Not too long [now]. We're just managing it at the moment."