Rotten Deals are deals that have been open for more than a certain amount of time. You'll be able to tell a Rotten Deal straight from the Deals Pipeline by the red "rotten" icon on the left of a deal's name.
You can specify the time after which a deal goes rotten. Hover the cursor over the Gear Icon next to your profile picture and choose Settings. From the list on the left, click on Deal Age. Type in the number of days after which an open deal will become rotten. Save