One of the most difficult was deciding to hold out All-Star right fielder Jay Bruce.
Bruce was hitting .318 in his past 13 games entering Friday, including three home runs, nine RBIs and four doubles.
But with Wandy Rodriguez taking the mound for the Pirates, Baker played the matchup and left Bruce out of the lineup.
Bruce has faced Rodriguez 29 times in his career and has recorded just two hits off him while striking out 15 times, holding a .069 batting average.
"That was another tough decision," Baker said. "If it was playoff time, would I have opted for Jay? I've got some other guys who hit Wandy well. I'm trying to downplay the series, because he's been relaxed most of the time."
Chris Heisey, who was hitting .357 with a home run and four RBIs in 15 at-bats against Rodriguez entering Friday, started in Bruce's place.