The classic description is here:
http://www.midweekclub.ca/powerFAQ.htm#Q23
However, I would slightly amend that procedure. It's kinda hard to balance on a pedal while the crank is exactly horizontal, so this is what I do:
1. Use a known weight (like barbell plates).
2. Clamp the bike into a trainer but back off the roller pressure so the rear wheel turns freely. Hang the weights from one of the pedals. Place the PT into torque measuring mode. Backup the rear wheel very slowly until the torque reaches a maximum. That will occur when the crank is horizontal.
3. To check linearity, repeat for a couple of different cogs. Doing it this way is easier than changing the weights for the same cog.