I might be fundamentally misunderstanding something, but I’d like to perform Topic Modeling with Amortized LDA and when I run through that tutorial on my own data, the setting up the model includes a line that says
No batch_key inputted, assuming all cells are same batch. I thought it might be a good idea to include a batch_key (as I have batches) but discovered I was unable to pass one as I did when setting up an scVI model.
Should I be able to provide a batch_key or is this something that isn’t appropriate for topic analysis? If it isn’t necessary, perhaps adjusting the info message to not say “assuming all cells are same batch” so that people don’t get worried they are missing something?