It doesn't matter which one is define first or second. It neither doesn't matter define which one is case or control. The only thing matters is how to interpret the result. Take your example: in the left frame, + indicate higher in control while in the right frame, - indicate higher in control. Asaf is right you should learn R and try to get the code from GEO2R and try to download and analysis the data more complicated. Don't use GEO2R all the time.