Finally, we evaluated whether any gene included in the reference panel was dominating the inference of cell proportions. We re-calculated the cell-type distributions of the chimeric libraries but dropping each of the genes from the reference panel one at a time. We observed a negligible difference between the cellular population structure inferred using the full reference and the gene-dropped panels (average RMSE = 0.022, s.d. < 0.01). In this way, we verified that the proportions inferred using the reference panel are not driven by the expression of a single gene. This reassured us the inference should be robust to any bias introduced by the potential association of a single gene included in the reference panel with a particular trait.
