I rented a room in my apartment and did not receive all of the rent due to me. I am having trouble figuring out how to take the loss of income on Schedule C or E.

When you "Don't get" income, you don't deduct it. You can't deduct something you never got.

Bad debt is different. You have something, money, that you earned and you paid taxes on. 

You lend it out, but it is never paid back. You lost money.

You never got the rent, so you never paid tax on it and you never lost it.