Carpets contain chemicals as well as the material they used to make the carpet.
Clean carpets regularly, and before you can visibly see dirty spots on it. We don't wear shoes in our house, but I still clean the carpets at least once-a-month in the high traffic areas. Cleaning your carpets regularly should also minimize the allergy symptoms you may be experiencing.
I run the iRobot in our bedroom at least 2X's a week.