OP didn't say why they changed out the RD, either.... An upgrade? Or was the old one damaged? Especially if it was damaged, I agree about having the derailleur hanger alignment checked. It's easy to do, but you can't just eyeball it and need a tool that costs $50+ to check and adjust the hanger. Once set, it usually won't need attention again unless it's tweaked in a fall or something like that. So for most folks it's most cost effective to give a few $ to a local shop to have them check it and adjust if needed.
Also be sure your wheel is fully seated in the drop-outs, not sitting slightly askew (usually this causes other problems, too).
Other stuff...
1. How old is your cable? Did you reuse the existing one? Any corrosion or kink in the cable, or just a lack of lubrication, can cause shifting issues ranging from minor to not-so-minor.
2. When is the last time you cleaned and lubed your chain? That's another seemingly simple thing that often leads to poor shifting. New chain? They come with a preservative on them, aren't actually lubricated, and should be cleaned and oiled carefully before use (I've been using Chain-L lately and really like it). While you're at it, is the cassette clean?
3. Have you put some drops of oil on all the derailleur hinge points? A little lubrication there can often do wonders.
4. Are you cross chaining? I.e., is the noise you hear occuring only when the chain is on the larger chainring up front and the largest cog at the rear? This is a combination that shouldn't be used. Usually when it's done the noises are actually coming from the chain rubbing on the front derailleur cage, but can be mistaken for rear der.
5. I disagree... It could be the H limit screw preventing the chain from seating fully on the cog with a normal shift. Easy to test. Just back the screw out (counterclockwise) a quarter turn or less. If the noise goes away, problem solved. If the noise continues, then it's something else. When installing a different derailleur, both the limit screws need to be set from scratch. Once set up, they seldom go out of adjustment unless something else changes. The limit screws simply do what the name implies... limit the swing of the derailleur to prevent it from moving too far at either extreme, which would move the chain past the most extreme cogs.
6. It might be the B screw needs a little adjustment, particularly with a new installation. This screw is the one that determines the tension in the derailleur, located up by the derailleur hanger and usually unmarked... Since the noise is happening only on the largest cog, it might be set for slightly too much tension. Try backing it out 1/4 to 1/2 turn (counterclockwise) and see if that makes a difference. If not, reset it. Then try 1/4 to 1/2 turn in (clockwise) to increase tension and see if that makes any difference. If not, reset it.
7. After eliminating all the above as possibilities, now it's time to try the barrel adjustment. Lengthening the cable housing (by turning the barrel counterclockwise when viewed from the rear) a click or two will increase the tension on the cable slightly, and might do the trick.
8. Finally, with new parts sometimes it just needs a little while for things to fully mesh and "learn to play together well".