As a rule rats should not make noises. You may hear an occasional squeak, chirp and so forth, but I think you are correct that the noise you describe may very well be from illness. Does your Brooklyn have other symptoms such as porphyrin staining, congestion, lack of appetite or lethargy? These could also be indicative of an illness. There are two rat sites that have audio clips that might help in determining what the noise means until you can get an appointment with the exotic vet. The links follow:
http://www.joinrats.com/gallery/11128370_reY4p#!i=801108532&k=uBgFS
http://www.ratbehavior.org/norway_rat_vocalizations.htm
All rats and mice carry the bacteria mycoplasma pulmonis. When a rat gets a mycoplasma infection, there is also a chance she will get a secondary infection. Baytril and Doxycycline are two antibiotics often prescribed together, but there are many other effective medicines, too. It all depends what kind of respiratory infection(s) is involved. Following please find details on mycoplasma/respiratory infections, pneumonia and secondary infections:
http://ratguide.com/health/bacteria/mycoplasma_mycoplasmosis.php
http://www.rmca.org/Articles/respir.htm
http://www.ratfanclub.org/resp.html
http://mia-carter.suite101.com/mycoplasma-and-respiratory-infections-in-rats-a68450
http://ratguide.com/health/lower_respiratory/pneumonia.php
http://ratsauce.com/sick_rats/general.php#cat0_5
I know I gave you as lot of reading material, but it is well worth the time. Also, trying to understand respiratory illness in rats and mice can be overwhelming and confusing, in my opinion, and the above articles do a good job of explaining it.
One last link I shall give you has proven invaluable to me. It is a rat medication chart. It details the various medicines along with what they are prescribed for:
http://www.rattie-express.com/Med_Chart.htm
I am sorry your Brooklyn is having a problem. I hope she is better soon.