Lisa, I have to agree with Jim on this.
You my have a rough idea regards the time it would take to do the deep clean and be more inclined go for a fixed price, over an hourly rate.
However from my own experience of deep cleaning factory's and offices over the years, I would go for an hourly rate, as the fairest option. In my experience it will always take longer to do a through deep clean than you may at first have thought when you looked over the job and priced it. As you begin the deep clean, you will find a lot of things you may not have budgeted for in your initial survey and quotation.
To do a through deep clean will take a lot of time, speaking from my own personal experience.
Good luck Phil