how to make one condition as a reference

[theislab]

how to make one condition as a reference

[johannesostner]

Hi!
The reference in scCODA is not referring to a condition, but rather a cell type. This is necessary, since single-cell sequencing population data is compositional, meaning we can only interpret changes with respect to a fixed reference category.

From what you describe, I assume you have one covariate (column in data.obs, let's call it obs1) with values cond1 and cond2, and you want to compare these groups. To set e.g. cond1 as the "control" group, you can modify the model formula to "C(obs1, Treatment('cond1'))". Otherwise, simply the value from the first sample in your data is taken as the control. See also the advanced tutorial (https://github.com/theislab/scCODA/blob/master/tutorials/Modeling_options_and_result_analysis.ipynb) for an example.

[FADHLyemen]

thank you, that helps