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Are you exposing all users to the experiment on the front end and then only tracking 10% of them in the data warehouse?

With our setup we could either do full exposure or exposure to just the tracked cohort. (Right now we're running tests on the full population using Game Analytics, which is extremely limited but free)

Ok, I'd probably recommend only exposing the tracked cohort to an experiment. As long as your sampling is truly random, it shouldn't be an issue statistics wise.