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Wigan's Emmerson Boyce tripped Wayne Rooney in the box and double-player of the year Ronaldo calmly sent the keeper the wrong way from the spot.
It was the Portuguese winger's 41st goal of the season for United and 31st in the league.
United had further reason to thank the referee soon after when he opted not to show Paul Scholes a second yellow card for a body check that could easily have ended his involvement.