I would put the message in the location that the user would expect to see the chart or if there is a standard error message area already in place in your application (e.g. the Firefox application has a standard error bar) then I'd use that. As far as what to say, be sure to tell the user how to get what they want (i.e. how to fix the problem) or if the data is not available and they should return later tell them to do so, and tell them why so they don't just think it's a bug.
Some examples of messages you might use:
You must select ona numeric value to use as a measurement and one field to categorize the numeric measurement.
There is no data available for the time period you have chosen. Please choose a different time period.