Portal 2 story line.....?

I'm not sure if there's something that I'm not getting or what, but first this is what I know of the story line: I know about everything in portal 1 and read what happened prior to it, and that after the comic "Lab Rat" (which is right after Portal 1) is when Portal 2 takes place and the game will start some where near you waking up GLaDOS. But I noticed that in the comic when "rat man" is running back inside Aperture Science, GLaDOS is still there, which, as far as I know, GLaDOS is supposed to be dead (as seen in the youtube video) until you waken "her" in Portal 2, which takes place after Lab Rat. So, why is GLaDOS alive in Lab Rat if she's supposed to be dead until Portal 2? Is there something that I'm missing or will Valve probably just explain that when Portal 2 is out?