Canon[Wikipedia] is the official version of a IP's backstory. That is, the elements of the Lore and fluff of a fictional universe's (such as Warhammer) backstory which are officially endorsed as the truth (in a fictional context) by the creators of the IP (Intellectual Property).
Canon in WarhammerEdit
Though there is a vague canon in Warhammer, many versions of different stories in the Lore differ, especially regarding the racial perspective from which the Lore is written. It has been said that "Warhammer is Batman", meaning that "anything goes". Though WAR draws from the Warhammer fantasy universe, it takes place in it's own setting called the Age of Reckoning, which bends the Lore of Warhammer and in some cases breaks the canon, to better suit the creation of a MMORPG computer game.