Why were the slaves in the beaufort and port royal areas not affected by the issuance of the emancipation proclamation? is it because they lived under union control?

The Emancipation Proclamation only freed slaves in Southern controlled areas. Areas like New Orleans, even though in the South, was under Union control when the Proclamation was given so technically none of those slaves were free. However, every other slave in the state of Louisiana was free. 

Lincoln did this so that he wouldn't anger those in the border states that hadn't officially joined the South, even though many of the men left to fight for the South.