I would suggest you go back to the doctor and discuss your concerns with the person that prescribed the medications.
My understanding is that metformin is a new treatment, sometimes prescribed to reduce the effects of polycystic ovary syndrome. Apparently it reduces blood clotting - which is your problem.
More information on this website:
Treatment of Polycystic Ovary Syndrome with Insulin Lowering Medications
However, your best option is to talk to the doctor and get her to fully explain the mediation, its positive effects and its side effects.
Good luck.