Use made of to talk about the material of an object – wood, plastic, glass, crystal, etc. which has not gone through very much processing. You can still see the original material:
– This table is made of wood.
– The window is made of glass.
– This shirt is made of cotton.
Use made from to talk about one object that came from another, different object:
– This purse is made from recycled plastic bags.
– Cheese is made from milk.
– Wine is made from grapes.
In each of these cases, you can’t see the original materials anymore (plastic bags, milk, or grapes); they have been transformed into something completely new.