Which model of MacBook Pro were you considering from the Apple Store online?
And what country or region (if not the USA) are you located?
The availability of certain models and configurations may vary in other locations.
The Apple Store online has changed; usually once you've selected an item to buy
you can add extras before the sub-total is addressed in the purchase final update.
So items such as applecare, storage drive upgrade, memory upgrade, & etc should
appear before the final page where you'd agree to buy from the online Store.
Since the option does not exist after the fact, with built-in RAM, details on which one
you are looking into, from the three main categories I see, in the US Apple Store,
are kind of important for anyone attempting to follow your question using that Store.
Compare a 13-inch and 15-inch model MacBook Pro, in store:
http://www.apple.com/mac/compare/results/?product1=macbook-pro-retina-13&product 2=macbook-pro-retina-15
Usually if you choose 'Buy' other options appear in the tally window, with change in price.
See base 13-inch + 16GB RAM option:
http://www.apple.com/shop/buy-mac/macbook-pro?product=MF839LL/A&step=config
Hopefully the model and configuration you need is available. Some actual official
Apple retail Stores may also have an upgraded model in stock...
Good luck! 🙂