Danila

Hey @Marius1311, thanks for the great point! Do you think there are use cases that you can share? It would be great to understand the context better to see how...

Hey @borauyar, It would be great to see how MOFA performs on unseen data! And I don't think I saw any public tutorials on that myself. As in the MOFA...

Thanks, Christian! This is caused by 116f6e6778c3aef6bf286c5f62c1a9a1efa4a29d indeed. @rargelaguet, I would consider to roll back this default setting back to `TRUE` in v1.8.1. And I think we would also be...

Thanks, @BenjaminDEMAILLE! From the last code snippet, this is basically what the MuData/AnnData stack already provides: ```py mdata["RNA"].layers["counts"] mdata["RNA"].layers["lognorm"] mdata["RNA"].X mdata["RNA"].var ``` I believe all the three points about flexible...

Hey @hsiaoyi0504, This is correct that there's actually no functionality to write or modify the model file in R (natively). The training is done in Python (with mofapy2), and this...

One thing to try could be training a MOFA+ model and seeing if the first few factors correspond to batch effect — and if the other factors correlate with the...

One of the ways would be to only keep some [highly variable features](https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.highly_variable_genes.html) (e.g. top few thousand genes and e.g. top 10k CpG sites).

Hey @jefferyUstc, thanks for reporting this. So far I wasn't able to reproduce this error. Is there any data that we could reproduce it on? Does it also happen with...

I don't know if the issue has been because of this being an *unpaired* dataset as this isn't multimodal data, which `mu.pp.neighbors` and the rest of the package have been...

Interestingly enough, `_scatter_obs()` supports it so this should be a very quick fix to account for the fact that `color` is not necessarily a string in `scatter_obs()`.