Rovers were beaten for the third time in their past five matches, with striker Dean Ashton grabbing the winner seven minutes after his arrival as a half-time substitute.
"In the first half West Ham had a lot of players behind the ball," remarked Hughes. "They stopped our influential players getting into the key areas, and they did it very well, with Danny Gabbidon and Matthew Upson outstanding. So credit to them. They worked extremely hard."
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