This is normal. You have a new pig.
It takes time for them to feel comfortable with you. It takes time and patience.
I have had Alfonz since March, and he still hates being picked up. I find he is a little more calm about it if I can get a hand under his belly, and one under his bum, they really dont seem to like any part of their little bodies to hang unsupported.
Be calm with her, like I said you could stop picking her up, and just get her used to your hands in the cage, sit and read her a book, sit and tell her about your day, put your hands in the cage, be calm, dont try and pick her up every time your hands are in there, sometimes just reach in to move her bowl, or move her house to the other side of the cage, sit with your hands in there with some tasty vegetables. Guinea pigs require patience, patience and more patience. Imagine you were the pet of something 32 times your size, you would likely run away too, until you grew accustomed to things.