In DeseqDataSet documentation, ref_level is described as below:
ref_level : list or None
An optional list of two strings of the form ["factor", "test_level"]
specifying the factor of interest and the reference (control) level against which
we're testing, e.g. ["condition", "A"]. (default: None).
Use of "test_level" in the example while requiring reference level is confusing. It will be better if the example is ["factor", "ref_level"] (like in the description of build_design_matrix) or ["factor", "reference_level"].
In DeseqDataSet documentation, ref_level is described as below:
ref_level : list or None
An optional list of two strings of the form
["factor", "test_level"]specifying the factor of interest and the reference (control) level against which
we're testing, e.g.
["condition", "A"]. (default:None).Use of "test_level" in the example while requiring reference level is confusing. It will be better if the example is ["factor", "ref_level"] (like in the description of build_design_matrix) or ["factor", "reference_level"].