I had a few questions about the
get_normalized_expression function that I hoped to get some clarification for. From the totalVI tutorial (CITE-seq analysis with totalVI — scvi-tools),
n_samples is set to 25 and
transform_batch is given the list of both datasets.
n_samples refer to the number of cells (surely it can’t be number of biological samples, as the example dataset only has 2 individuals?), and if yes, why is the default 1 / why is the suggested number in the tutorial 25 / what might be a recommended number to set this as?
Second, how exactly should the
transform_batch argument be used? I understand from the documentation and github (how to get corrected expression matrix after batch removal · Issue #786 · YosefLab/scvi-tools · GitHub) that it is about which batch to condition over. Intuitively, it seems to be that it would make the most sense to condition over all the batches as is also done in the tutorial, but would there be any situation where that might not be recommended?
Many thanks in advance.