Saturate the edge of a paper towel with isopropyl rubbing alcohol. This alcohol is diluted enough to make it safe for the transparency and will effectively remove the ink.
Rub the damp paper towel over the transparency, using new sections of paper towel as the ink is removed.
Dip a cotton swab into the alcohol to rub over small areas of the transparency when you need to make small corrections. This allows you to correct small errors without removing ink from large sections of the transparency.