What is the difference between paired and unpaired and same.dir is true or false in Gage?

Question

[Tania]

Hi Everyone

What is the difference between paired and unpaired and same.dir is true or false in Gage? I read the manual of gage but I still don't get it. If anyone can help me with a nice example. Gage will look for pathways any of my gene list are involved in, so what does it mean same direction or both, paired or not?

Thanks