Beta from comps in different regions/markets

Hi guys, got a question for beta calculation. I had my comps set downloaded from CIQ, and was about to start the unlever - average -relever exercise to calculate the beta for the target company. However, I just realized that my target is an EMA company, while many of my comps are across US/Europe. Even I can make up for the equity risk premium in the emerging market, I am not sure about the exercise now because the comps betas may have been off different equity indexes, in case it matters. Could someone enlighten me on how to calculate the beta when target and comps are in different markets and may be based off different equity indexes?

Thanks very much!

dias