Didn't Valve say that the events of Portal and Portal 2 weren't cannon with the Half-life universe but Aperture Science is?
They are both canon, Valve hasn't said anything like that at all. If Portal 1 and 2 aren't canon, then what would we know about Aperture Science? Nothing at all. However:
GR: From the design standpoint of Portal 2, were you are thinking in your mind, “if we were going to make a Half-Life 3, how would Portal 2 tie into that main story line?”
EW: Yes, to a certain extent, you don’t want to do something that is going to screw up Half-Life 3. So I can tell you that Chell is not going to blow up the Earth by the end of Portal 2. You want to leave something there. But having said that, we do the linkage and do some references but we kind of considered, at least Portal writers do, [that] if you think of it as the X-Files, Half-Life is the ongoing serious story with the characters of X-Files. Then X-Files would have these absurd one-off episodes. Portal is a self-contained thing and that’s the Aperture Funhouse of Science, you know?
This does not suggest it is non-canon at all though. It just means the things that happen in Portal 2 will not have a direct impact on the next Half-life game, other than a few things about Aperture science itself and maybe a few references to Portal 2.
Portal 1 is cannon. Portal 2 isn't
That hasn't even been suggested by Valve.