Error when subset RNA assay stored on-disk

[nimanouri-nn]

Hello BPCells,

I was wondering if you could please take a look at my issue regarding Seurat or possibly BPCells. I am not certain which one it relates to more, but your advice would be greatly appreciated.

[bnprks]

Thanks for linking this issue. At the very least the misspelled error message is mine :) (Should say "Col" not "Cow").

I did just make some changes to the subsetting logic in BPCells, which is a good candidate for what might be causing this bug. However, I've been unable to reproduce the error with some initial attempts on my end.

Is there any chance you could put together a reproducible example? See here for a good example of using Seurat's demo pbmc3k dataset to hit an issue. You might consider "merging" pbmc3k with itself once to simulate your multi-sample dataset.

A second-best option would be if you can share the code that you're using to process your dataset, which might provide some clues of how to hit this error.

Once I can reproduce the error on my end, I'll be able to much more easily poke around in the object internals to see where things are going wrong. I strongly suspect that this error is not caused by the fact your data was stored on disk, but is some intermediate bug in BPCells triggered by the way the data was handled in Seurat.

[bnprks]

Actually, I think I just found and fixed a likely culprit for this bug. I've now pushed an updated version of BPCells to github -- would you try reinstalling BPCells and check if that's fixed your issue now?

[nimanouri-nn]

You are the one! Thanks for the prompt fix. It's working properly now.