Graphpad is designed for statistical analysis. It has some really complicated analysis tools for those apps. However it is NOT easy to wade through all that mess to do something simple like take one column and subtract it from the other.
To do simple stuff like that click
then select the data sets to be included then click
>Remove baseline and column math (Transform, Normalize list)
Click the column you want as the base (for instance the column containing the exact solution)
>Calculation (pick your operation)
>Create new graph of the result
that's it. I'm not sure how it handles negative numbers exactly. you might have to create another column or do it by hand.