This can be achieved fairly easily. I'll try to explain it.
1) Create the event that will act as your "shop."
2) Text saying "Hello, and welcome...blahblahblah... What do you want to buy?"
3) Display Chices, "Item 1, Item 2, Item 3, More" (If you want 4 items, replace more with 4)
4) When 1: Text: "You want Item 1? It will cost 3 potions!"
5) Show Choices, "Buy, Do not Buy"
6) When Buy:
Variable Operation: (this is where XP,VX and VXA difer slightly) Set variable 1 to the number of potions present.
VX: Control Variables, Set, Item: 001: Potion in Inventory
VXA: Variable Operation: Substitute, Game Data, Item, 001:Potion is Present
7) Conditional Branch: Variable 0001 is equal to or greater than 3 (since Item 1 costs 3 potions)
Be sure to check "Set handling when conditions do not apply"
8.) When conditions met, Add Item 1, Remove Potion x3
9) When not met, Text: "You dont have enough Potions"
Repeat this process for all the items.
It is VERY complicated to some people but once you gain experience in how RPGMaker works, its fairly easy to do just about anything. If you still don't understand, I can record myself doing it on video and post it here so you can see it better. =D