What does the noise sound like? Is like a coughing noise or a gagging noise? What type of dog is she? It's possible she has a collapsing trachea, which sounbds serious but is, in fact, very common in small breeds. Larger dogs can also have it but it's far more common among toy breeds.
As I said, it's not a serious condition but the noises can sound scary from time to time. Usually an episode of the noises will occur when the dog is excited over something. It's not all that common for it to happen when the dog is relaxed or sleeping.
Ghilly
Have you had her to a vet yet? She just might really have something stuck in her throat. :-)