Pseudobulk issue?

[saezlab]

Pseudobulk issue?

[PauBadiaM]

Hi @jackbrougher,

Thanks for checking out the package! What version of decoupler are you using? I would recommend installing the latest one using:

pip install git+https://github.com/saezlab/decoupler-py

There was a bug in the get_pseudobulk function in version 1.0.0 that should be fixed now. Else, just curious, what is your bulk_labels indicating, cell type?

[jackbrougher]

That checks out! I updated and the command ran! Now I just need to figure out where I'm off before that to be getting an empty dataframe when computing DEA's.

And yep - bulk_labels is my cell type label.

[PauBadiaM]

You can get an empty data-frame for different reasons, actually I will implement some warnings for when these cases happen to make it more informative. The reasons can be:

• You don't have enough samples to do a comparison. To make one, you need at least 2 samples of each group (at least 4 samples in total).
• The condition or the reference labels are not in condition_col.
• group_col and condition_col need to be different.

Maybe you could post the line of code that you are using so that I can see it.

[PauBadiaM]

I added some warnings in the function to better know what is going wrong, you can test it if you install the latest version again. Hopefully it makes it clearer!