The testimony of Brian McNamee, the former trainer of pitcher Roger Clemens, who is on trial for perjury, did not match the testimony McNamee’s wife gave on Wednesday. (Haraz N. Ghanbari/Associated Press)

The estranged wife of Roger Clemens’s chief accuser testified Wednesday that her husband did not initially confide in her about injecting big league ballplayers with performance-enhancing drugs, contradicting his account of how and why he kept needles, cotton balls and other medical waste from injections he allegedly gave the star pitcher.

Former strength coach Brian McNamee is considered a key prosecution witness in Clemens’s perjury trial, now in its eighth week. He is the only person to testify to firsthand knowledge of the pitcher’s alleged use of performance-enhancing drugs. Clemens is charged with lying to Congress when he told a House panel in 2008 that he never used steroids or human growth hormone.

During four days on the witness stand, the strength coach testified that he saved the medical waste in a FedEx box to appease his wife. Brian McNamee said there was tension in his marriage because his wife was concerned that the strength coach would take the fall for the star pitcher if Clemens ever got in trouble for using the banned substances.

But Eileen McNamee, who took the stand for the first time Wednesday, told jurors that she did not initially know what was in the box she discovered in their basement closet in 2001.

Her husband said “he was saving things for his protection and it was none of my concern,” Eileen McNamee testified.

Her husband only confided in her about the alleged injections a few days before a report by former senator George Mitchell identified dozens of ballplayers, including Clemens, as performance-enhancing drug users, she testified.

Eileen McNamee pointedly refuted her husband’s claim that she was harping on him because she feared he would get in trouble.

“I couldn’t tell him to stop doing what I didn’t know,” said McNamee, who agreed to testify after receiving an immunity agreement from the Justice Department.

The defense team is trying to convince jurors that Brian McNamee is not a credible source in part because of alcohol and drug problems. Eileen McNamee, however, said that her husband was only drinking “moderately” in 2001 when she asked him about the FedEx box.

Attorneys for Clemens also tried to cast doubt Wednesday on the key physical evidence against Clemens. The defense’s DNA expert, Marc Taylor, took issue with the prosecution expert’s assertion that it was virtually impossible for someone to intentionally plant Clemens’s DNA from one of the cotton balls on the needle. The DNA on the needle could also have come from more than one person, Taylor testified.

The defense expert did not dispute the results or conclusions of the analysis by the prosecution’s witness and acknowledged that he did not do any of his own testing on the physical evidence.

U.S. District Judge Reggie Walton displayed little patience from the bench Wednesday, particularly for the defense team. With jurors out of the courtroom, he chastised Clemens’s lawyers during an exchange about Eileen McNamee’s testimony.

“I don’t know how you all practice law down in Texas,” the judge said to Rusty Hardin, Clemens’s Houston-based attorney.

“The same way,” Hardin replied.

“Don’t look at me like you’re going to intimidate me, sir,” Walton said. He later apologized for the exchange.