That lineup had Lance Berkman slotted to play first base and bat in the cleanup spot. But after several tweaks and adjustments, the final product had Darin Erstad as the starter at first.
Cooper talked with Berkman, who is "a little banged up," on Saturday night. Berkman has been dealing with pain in his left hamstring, and about a week ago, he fell and hit his wrist at home.
Cooper said that Berkman will likely play Monday, but he decided to give him the day off Sunday after sleeping on the idea. The move had a ripple effect through the rest of the positions, with Mark Loretta at second base, Jose Castillo at third and Reggie Abercrombie playing center field and leading off.
The decision to put Abercrombie at the top of the lineup came down to something similar to a process of elimination.
"It isn't every day when you don't have one or two of your guys," Cooper said. "You always do that. You try to put the best guy you can in that spot. Hopefully, that spot comes up and it's the right scenario.
"We deduct and add and subtract, and we come up with it. And some guys are just better suited for certain spots."
With Berkman out of the lineup, the Astros will be without one of their biggest bats. He is hitting .331 with 26 home runs and 93 RBIs, and he went 4-for-9 from the plate through the first two games of the New York series.
Houston has already had to fill the offensive voids left by Kazuo Matsui and Carlos Lee, both on the disabled list -- Matsui with an irritated disk and Lee with a fractured left finger. Along with Berkman, those three players had been the meat of the Houston lineup.
"They're the biggest part of our offense. They're the guys," Cooper said. "It doesn't matter how good your bench players are, you're never going to replace those guys. No matter how well they play, they're just not going to replace those guys. They can't."
But while the reserves may not be able to equal the contributions, Cooper said they have delivered consistent solid performances, and he will continue to rely on them for all-around production.
"You just ask your extra guys to go in there, contribute a little bit, maybe each get a base hit somewhere, score a run, just like they've been doing," Cooper said. "They've been doing a bang-up job."
Samantha Newman is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.