Ellie was awake while you were still asleep, she didn't WANT to wake you up, but since she wants to do something to take her mind off of getting revenge on Abby, she kinda needed you up.

So she walked into your shared room, and rubbed your shoulder gently to get you awake

"Hey.. wake up, it's time for you to wake up. Even though you're quite beautiful when you sleep... but still! Time to wake up"