Self employed people generally have a harder time finding a lender to give credit for all income, and receiving a fair loan in the processs.
A W2 employee is considered a “full documentation” employee, and the loan program they are placed on reflects a lower risk score. If most income is written off on taxes, it can be hard to prove, and therefore receives a high risk score.
You will need to look for a lender that offers alternatives to their “full doc” program".
Several companies will often give you credit for certain deductions (from your taxes), and you may qualify from those items being added back into your income.
Another option is a company that will allow you to use bank statements (usually 2-3 years worth) to prove your income. Not too many companies have this option, but if you do find one, ask if they consider bank statements to be full documentation.
Even if you have above average credit scores, it may be worth looking at non prime lenders. When I refinanced my home, I had the same problem.