I'm not sure what exactly OP is referring to, but there is a difference in the nutritional data of, for example, raw chicken breast (which is marked on the packaging) and baked chicken breast (which is what gets digested [unless you actually eat it raw]).

See http://nutritiondata.self.com/facts/poultry-products/701/2 VS http://nutritiondata.self.com/facts/poultry-products/703/2

Make sure you line up the serving sizes.