@@ -1295,6 +1295,7 @@ List GxE_fitness_score_mvlm(NumericMatrix case_genetic_data_,

         // arma::mat x_vec_lengths = join_rows(x0_orig, mean_vec_lengths);

         // arma::vec beta_prob_disease = solve(x_vec_lengths, prob_disease, solve_opts::fast);

         arma::vec beta_prob_disease = solve(x_orig, prob_disease, solve_opts::fast);

+        double beta_prob_disease_int = beta_prob_disease(0);

         // make sure association is positive 

         // bool pos_assoc = beta_prob_disease(1) > 0;

@@ -1351,6 +1352,9 @@ List GxE_fitness_score_mvlm(NumericMatrix case_genetic_data_,

         s_vec(1) = ht_trace;

         arma::vec centered_vec = s_vec - null_means;

+        //reset the correct intercept

+        beta_prob_disease(0) = beta_prob_disease_int;

+        

         //make sure the elements are both greater than the random nulls, otherwise

         // set to small value

         bool neg_elem = any(centered_vec <= 0);