Subtract a vacancy and collection amount and then operating expenses to get NOI. 

I subtract it from the deposit if I select them as a tenant otherwise I don’t do anything.

Would you subtract the project cost straight from your purchase price?

Take gross rent,Then subtract your costs like tax and insurance, water, electric, repairs.

If you are taking the potential rent and subtracting her current or potential new mortgage payment, that is not a relevant exercise to determine if it is a good investment.There are weekly posts on BP from new members wanting to convert their old primary residence to a rental and, in many cases, it's a bad investment decision and, in all cases, it's limiting (only one property is being analyzed).  

@Robert McDowellThe starting point for NY Taxable income starts with Federal taxable income.New York then requires "additions" and "subtractions" to the federal taxable income based on the difference in Federal/New York Tax law differences.Form number IT-225 lists all the additions/subtractions there are for New York State.The section 121 exclusion is not an addback for NY Purposes.https://www.tax.ny.gov/pdf/current_forms/it/it225i.pdf

Payout = $19,000ACV - will pay out $20k minus a depreciation factor (probably 50% depreciation on a 15 year old roof) then subtract the deductible.Payout = $9000Leaving the property owner paying out of pocket $11,000 to fix the roof.Big difference right?

I would look at the value Zillow  or Trulia gives it, and then subtract from that value the cost of repairs needed.

Subtract future expenses from the income.

I will take my 240K a year gross rents, subtract all expenses, including debt, and then look at my results.