The Baggies were beaten for the second time in 72 hours thanks to a late goal from Potters substitute Dean Whitehead as they dropped to fifth spot in the Premier League.
Clarke made six changes from the line-up beaten 3-1 at Swansea on Wednesday and left out key players Peter Odemwingie, Roman Lukaku, James Morrison and Chris Brunt.
But he is adamant the Baggies have sufficient strength in depth to cope with such alterations.
Clarke said: "I've got a good squad. I've always said that. There are players there that deserved to play, others who were a bit tired after the previous two games.
"I made the decision to shuffle the pack a little bit. I don't think that was any reason for the defeat against Stoke.
"If you look at the balance of the squad over the whole week, it might have seemed like a lot of changes.
"But some of the boys who played against Stoke actually played last weekend as well (against Sunderland).
"I thought it was the right time to freshen the team up."
Clarke is determined to stay as level-headed about successive setbacks as he was when West Brom won four games on the trot to move into the top three.
He is confident of obtaining a positive response from his side who visit Arsenal next weekend.
He said: "We lost two games earlier in the season and bounced back with four wins.
"I'm not saying we are going to do that again but we are certainly going to bounce back.
"We are a good team, we are in a good place. We've worked hard to be in a good place and have a good points total.
"We're happy to be here in this position at this stage of the season but we are not happy because we want to do better.
"But I told the lads after the game they have got nothing to be down about.
"We got 12 points out of 15 during November, a great return, and the lads should be positive going into the rest of the month.
"Certainly their head coach certainly is. I know I've got a good group of players."
Clarke added: "We always tried to downplay where we were and what we were doing.
"We didn't get carried away when we were winning every game and we try not to get too despondent when we lose a few games.
"That's the way we try to work from inside. If people want to talk about us, we can't do anything about that. We can only do what we can do."