As expected, New England Patriots quarterback Tom Brady on Thursday appealed his four-game suspension by the NFL for his role in the DeflateGate scandal. The appeal was filed on behalf of Brady by the NFL Players Association, which called on NFL Commissioner Roger Goodell to appoint an independent arbitrator to hear and resolve the issue.

NFL spokesman Greg Aiello confirmed late Thursday that the commissioner had rejected that request and will personally hear the suspension appeal of the Super Bowl MVP.

“Commissioner Goodell will hear the appeal of Tom Brady’s suspension in accordance with the process agreed upon with the NFL Players Association in the 2011 collective bargaining agreement,” Aiello said. Goodell’s decision was first reported by the Bleacher Report.

Union officials declined immediate comment. Patriots team officials and Brady’s agent, Donald Yee, did not immediately respond to emails from the Associated Press seeking comment late Thursday.

While the collective bargaining agreement gives Goodell control of the arbitrator, the players union said in a news release that “given the NFL’s history of inconsistency and arbitrary decisions in disciplinary matters, it is only fair that a neutral arbitrator hear this appeal.”

If the league and its investigators are truly confident in their case, the union said, “they should be confident enough to present their case before someone who is truly independent.”

The union did not detail the basis for the appeal. But in a 20,000-word rebuttal posted online by the Patriots’ lawyers earlier Thursday, the team disputed the conclusions on matters of science, logic and law.

Yee previously had said that Brady would appeal the suspension, which is to be without pay and, if it is not reduced, would cost Brady about $1.88 million. Jeffrey Kessler, one of the union’s outside attorneys, is to assist in Brady’s appeal.

The appeal has to be heard within 10 days, either by Goodell or a person he designates in consultation with NFL Players Association executive director DeMaurice Smith, according to a report by Bloomberg News.

If Brady is unsuccessful with his appeal, he’d miss the opening game of the regular season, a Thursday night meeting with the Pittsburgh Steelers on Sept. 10 in Foxborough, Massachusetts. The 10-time Pro Bowl selection could also sit out games against the Buffalo Bills, Jacksonville Jaguars and Dallas Cowboys, Bloomberg reported.

If Brady serves the full four-game ban, he’d be eligible to return on Oct. 18 against Indianapolis. It was the Colts who informed NFL officials that Brady and the Patriots were using under-inflated footballs in the conference title game.

The Patriots have not yet indicated whether they will appeal their $1 million fine and loss of first- and fourth-round draft choices.

But they are not merely accepting the conclusions in the report by lead investigator Ted Wells.

Far from it.

FORMAL REBUTTAL

The Patriots issued a formal rebuttal Thursday, publishing on their website a lengthy item titled “The Wells Report in Context” that attacks many of the points made by Wells.

“The conclusions of the Wells Report are, at best, incomplete, incorrect and lack context,” the response on the team’s website says. “The Report dismisses the scientific explanation for the natural loss of psi of the Patriots footballs by inexplicably rejecting the Referee’s recollection of what gauge he used in his pregame inspection. Texts acknowledged to be attempts at humor and exaggeration are nevertheless interpreted as a plot to improperly deflate footballs, even though none of them refer to any such plot. There is no evidence that Tom Brady preferred footballs that were lower than 12.5 psi and no evidence anyone even thought that he did. All the extensive evidence which contradicts how the texts are interpreted by the investigators is simply dismissed as ‘not plausible.’ Inconsistencies in logic and evidence are ignored.”

Wells concluded that the Patriots probably violated league rules deliberately by using under-inflated footballs during the AFC title game and Brady probably was aware of what was going on.

The Patriots said their response was written by attorney Daniel L. Goldberg, who represented the team and attended interviews of its personnel by investigators.

The team’s response attacks, in particular, the measurements of the air pressure in the footballs used by the Patriots during the game and Wells’s interpretation of text messages between team employees John Jastremski and Jim McNally.

IDEAL GAS LAW

The Patriots, in their response, continued to assert that the under-inflation of their footballs by halftime can be explained by environmental conditions.

“The Ideal Gas Law, according to the League’s consultants, establishes that the psi of the Patriots footballs at halftime would have been 11.32 to 11.52 due solely to the temperature impact on the footballs. . . . With the Logo gauge, 8 of the 11 Patriots footballs are in the Ideal Gas Law range and the average of all 11 Patriots footballs was 11.49 – fully consistent with the Ideal Gas Law’s prediction of exactly what that psi would be,” the team’s response says.

The Patriots, in their response, also say that Wells misinterpreted a text message in which McNally referred to himself as the “deflator.” According to the team’s response, that was in relation to McNally’s weight.