Not related to fishkeeping but when I bought my house (bank foreclosure) there was an area of mold in the laundry area, treating/getting rid of the mold was a very intensive process.
If you have mold that is causing your 'allergy' symptoms chances are it's not just in the carpet but also in/on the subflooring, cleaning the carpet won't do anything for this type of mold (it could make it worse as you would be adding moisture in the cleaning process - no matter how much carpet cleaning companies claim their process leaves carpets dry, moisture still gets through to the subflooring). If you want to be sure you really have to see under the carpet and any underlay, and if yours is the ground floor appartment you need to check in the basement/crawlspace if you have one.
If you have mold that is causing your 'allergy' symptoms chances are it's not just in the carpet but also in/on the subflooring, cleaning the carpet won't do anything for this type of mold (it could make it worse as you would be adding moisture in the cleaning process - no matter how much carpet cleaning companies claim their process leaves carpets dry, moisture still gets through to the subflooring). If you want to be sure you really have to see under the carpet and any underlay, and if yours is the ground floor appartment you need to check in the basement/crawlspace if you have one.