NEW YORK (CNN) -- New York Times reporter Judith Miller, who went to jail for refusing to reveal her source during an investigation into the 2003 outing of a CIA operative, has retired from "the old gray lady," the newspaper announced Wednesday.Her retirement takes effect immediately, according to the statement.There was no immediate comment from Miller, but in a letter to the newspaper -- scheduled for publication in Thursday's editions -- she said she was quitting because "I have become the news, something a New York Times reporter never wants to be."The 28-year veteran of the paper spent 85 days in jail for refusing to testify before a grand jury investigating who revealed the identity of CIA agent Valerie Plame. The agent's husband, Joseph Wilson, is an outspoken critic of the Bush administration. Plame's identity was leaked after Wilson, in a Times op-ed piece, challenged a key element of the administration's case for war -- that Iraq had sought uranium from Niger for a nuclear weapons program. (Read Wilson's reaction to leak investigation)Miller, 57, was released from jail in September after her source signed a waiver allowing her to testify.Her source, I. Lewis "Scooter" Libby, Vice President Dick Cheney's then-chief of staff, was indicted October 28 on charges of perjury, obstruction of justice and making false statements to federal authorities investigating how Plame's name was leaked. (Full story)Miller was part of the team that won a 2002 Pulitzer Prize for its reporting on the al Qaeda terrorist network. However, her reporting on Iraq's weapons programs was widely criticized when no such programs emerged after the fall of Iraqi leader Saddam Hussein.The paper's executive editor, Bill Keller, was complimentary of Miller in a Wednesday memo to his staff. "She displayed fierce determination and personal courage both in pursuit of the news and in resisting assaults on the freedom of news organizations to report," states the memo posted on the Times Web site. Likewise, Times Publisher Arthur Sulzberger Jr. praised Miller's "significant personal sacrifice to defend an important journalistic principle." But Keller also points out in the Wednesday memo that Miller was "distressed" by a reference in an earlier memo to her "entanglement" with Libby and another reference stating she "seems to have misled" a Times editor. Keller clarified in his Wednesday memo that he was not implying her relationship with Libby was improper and that he was not contending she misled anyone.Miller's lawyer, Matthew Mallow, told CNN the war of words was trivial compared to his client's devotion to the First Amendment. "That's what Judy did with great courage, spending 85 days in jail. That is lost in all of the discussions of the internal workings of the paper," he said, adding that Miller left the paper "on an amicable basis."Miller said in her farewell letter to the Times that she was leaving with "mixed feelings."Mallow said he would neither comment on the terms of her departure, nor on discussions he and Miller's other representatives had with the Times about her decision to leave.