Position rack in middle of oven. Preheat oven to 350°F. Line 12 medium muffin tins with paper cupcake liners. Put grated apple in a small bowl and stir in brandy. Put flour, sugar, baking soda, salt, cinnamon, nutmeg and cloves in a large bowl of an electric mixer. Mix on low speed just to combine ingredients. Mix in eggs, oil, 1 ts vanilla, and apple mixture.

Divide batter among 12 muffin tins, about 3 tb batter each. Bake until toothpick inserted in center of cupcake comes out clean, about 23-25 minutes. Reverse baking sheets after 12 minutes, front to back, to ensure cupcakes bake evenly. Cool cupcakes for 5 minutes in pan. Transfer cupcakes in their paper liners to wire rack to cool completely.

Put butter, cream cheese, and 1 ts vanilla in large bowl of an electric mixer and beat on medium-low speed for about 1 minute until mixture is smooth and butter and cream cheese are thoroughly combined. Decrease speed to low and add powdered sugar in 2 additions. Beat until powdered sugar is incorporated and frosting is smooth. Spread cream cheese frosting over top of each cupcake.