Nurbol, the analysis will need to take account of all the costs of the equipment over its working life (purchase, running costs, maintenance and spare parts, reagents and disposables - baseline and per-analysis) as well as the staff and infrastructure costs involved in running the equipment. Cheap equipment which requires a higher labour input may not save money in the long run.
Some equipment suppliers use the 'inkjet printer' charging model - the equipment itself is supplied at a very low cost, but the price of essential supplies is very high, and increases over time.
Activity based costing (http://www.pearsoned.ca/highered/divisions/virtual_tours/horngren/man_acc/Ch05ManAcc.pdf) is one approach to assessing costs.
Dear Nurbol, In addition to previous authors suggestions, I would suggest that you set up a quasi-experiment study which has an intervention site and a control site. This will help you determine which local optimal conditions does your tools work. Regions, countries are different in a number of issues (these could be potential confounders) in explaining the outcome of your study.