"Whereby" means "by which."
The difference between the ablative expressions "by" and "with" are very small, but this might put it into perspective:
If you gathered the data in question yourself, you are calculating other things using your data, which means you should use "with which." If the data was not your own, you would make calculations based upon the data, and then would use "whereby." You could still make calculations "based upon" your own data, but because the data is specific to you, it would be better to use "with which" and not "whereby."
Essentially, "whereby" is impersonal, while "with which" is personal.