Can you describe that a bit more? Is it that the rim has a dip in it, or is there a lot of movement side to side and a sort of potato-chip shape? If there's a depression in the roundness of the rim, you might be able to make it somewhat better, although if the wheel is sound and you haven't been feeling it (and if your brake pads don't interfere with the tire at that low spot), you may not need to do anything other than make sure the spokes are evenly tensioned and the wheel is as true and round as it can be.