Side window won't go up
 

The passenger window won't go up and drops even further when I close/open the door. I did have a flat battery this morning and don't know if this has had an impact.

Just try a quick reset see how that works for you once you have charge back to your battery,press your window switch up till you hear a slight click then down again till you hear click again,if you had totally flat battery you may need to do both windows and a radio reset