The Gunners had a tough battle against one of the league's in-form teams as they were pegged back by the Bees.
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Arteta's side took the lead through new signing Leandro Trossard who scored his first goal for the club after a simple finish from a wonderful Bukayo Saka cross.
The lead didn't last very long, though, as Toney netted the equaliser following a scrap in the box, and Brentford were able to hold on from there.
Thomas Frank's side were able to threaten throughout the game, and will be happy to leave the Emirates Stadium with a point.
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Arteta spoke after the game and felt Toney's equaliser shouldn't have stood as he believed it was offside, seemingly due to Ethan Pinnock blocking Gabriel Magalhaes in the build up.
"I've just looked at it back, and it is offside," he said.
"If we apply what the referee tells us every single week before the game. If you are the blocker then you are offside. It's offside."
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Despite that, the Spanish manager praised his side's display: "I think it was a really strong performance, against a really tricky team to play against."
Speaking after the game, Trossard told the BBC that the Gunners wish to keep the momentum going despite the set-back.
The Belgian said: "Yeah of course it's nice to have the goal as it gets me going but after that it's disappointing they got the equaliser. It's a tough one to take. We did everything well. To score against Brentford isn't easy.
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"We said before on the set-pieces they're really good and today it happened again. We have to learn from that. There's a game again on Wednesday to turn things around.
"You don't get your way every game. We have to work hard every single day. There's a great atmosphere in the team and we have to keep that momentum going even when results don't go your way."
Arsenal next face Manchester City and will be hoping to win to keep their advantage in the race for the title.
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