I investigate a problem via a regression model. Firtsly, I have two different ways to measure my outcome, which I incorporate as a two-level factor variable X. However, each of these methods is again influenced by a factor variable with two levels, but these factor variables differ for each method. Thus, for the level X_1 I have "nested" categorical predictor levels "A_x1 and B_x1" and for the level X_1, I have categorical predictor levels A_x2 and B_x2.

How do I formulate this within a regression model in R? Can I fuse the levels A_x1, B_x1, A_x2, B_x2 to just one factor variable with 4 levels, or does this produce problems, because these levels mutually exclude each other regarding the levels X_1 and X_2?

Thanks!