Spot the Signs. The most obvious sign that you'll receive this reaction is if you haven't had a healthy relationship with your manager in the past. Maybe you continually challenged his ideas, and he took that as a sign of disrespect. Or, maybe she always made unreasonable demands, and you were never able to see eye_to_eye on your to_do list. Or perhaps his moods were completely unpredictable. In any case, if your relationship has been strained, you may receive a less_than_ideal response to your two weeks' notice.
Sure, it may sit in the depths of HR until the end of time, but you can be sure of two things: One, your former boss (and future reference) will read it and be impressed. And two, if you ever decide to come back to your company (hey, it happens), it's a very good thing that last thing on file is a great, professionally written resignation letter.