Can my wife conceive?

My 28 years old wife had a cyst so she underwent an operation last year. The doctor was supposed to do a laparoscopy but they found something else and operated the lower abdomen area. The reason they gave was there were bowels or something, which I did not understand. We have no baby and she still has two chocolate cysts in her left ovary sized 2.5 cm and 3 cm each. During her menses she complains about pain on her right side so the doctor has given her some painkillers. Can she conceive? Please advise.