Before we get to messing with limit screw adjustment I will assume that you have checked to see if your problem lies with just a slack cable, which is easily taken care of with a 1/4 turn or two of the barrel adjuster.
The picture on the right shows you the three adjustment screws that reside on your rear mech. From the top we have the B limit screw then the High limit screw and on the bottom the Low limit screw.
The B limit screw adjusts the height of the derailleur another way to look at it is the clearance between the cogs of your cassette and the top jockey wheel. Often the clearance is good until you change into the large low gear cogs and then you start to get a rumble as the jockey and chain is bumping along the underside of the cassette cog. If this is happening on your setup just turn that screw in clockwise to increase clearance. ideally we are looking for a gap of about 4-6mm. Sram works best at around the 6mm mark. Anyone using a Campagnolo system may have to search for the B limit screw, they have a few models with the screw mounted on the pulley cage behind the body and hidden from view.
Firstly loosen the pinch bolt on the cable to release it. Turn the pedal to bring the derailleur to its relaxed position which should position the jockey wheel under the small cog, the high gear on the cassette. If the derailleur shoots inward and comes to rest under the big cog, low gear, then you have a low normal derailleur. These are sometimes found on mountain bike setups. Whatever you have the principles are the same and I will cover them both. If the derailleur has come to rest under the small cog place a screw driver on the H screw, if it rests under the big cog then the Low limit screw. Stand behind the bike and adjust the screw in and out to center the jockey wheel perfectly under the above cog. As you turn the screw you will see the mech. move from side to side, use that movement to center the jockey wheel perfectly.
If you are sure of your adjustments and still the shifting is not as it should be then you may have some other problems. Most common is a bent derailleur hanger, which can be aligned, but takes a special tool to do so. Come see us and we can take care of that for you. Another possible cause is a bad cable or contamination in the housing. Easily rectified with a nice slick new cable and a couple of feet of Jagwire housing. Again we can hook you up.