Preheat oven to 375 F. Line 12 muffin cups with liners, or spray with baking spray.
In a large bowl, combine oats, flours, flax meal, brown sugar, baking powder, cinnamon, salt, baking soda, and cloves. Make a well in center of flour mixture; set aside.
In another bowl, combine eggs, milk, apple sauce, grated apple, and vanilla extract. Add wet mixture all at once to the flour mixture.
Stir just until moistened (batter should be lumpy.) Divide batter between 12 prepared muffin cups, filling each to almost full.
Bake for 18 to 20 minutes or until golden and a wooden toothpick inserted in centers comes out clean.
Cool in muffin cups on a wire rack for 5 minutes. Remove from muffin cups; serve warm.