de_out3 <- differential_expression_wrapper(expr_median = 
    expr_median_sample[functional_markers, ], 
  md = md, model = "lm", formula = formula_lm, K = K)

apply(de_out3$adjp < FDR_cutoff, 2, table)

adjp_BCRXLvsRef
FALSE               9
TRUE                5

## Fit a linear mixed model with patient ID as a random effect

de_out4 <- differential_expression_wrapper(expr_median = 
    expr_median_sample[functional_markers, ], 
  md = md, model = "lmer", formula = formula_lmer, K = K)

apply(de_out4$adjp < FDR_cutoff, 2, table)

adjp_BCRXLvsRef
FALSE               3
TRUE               11