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scverse / anndata

Annotated data.
http://anndata.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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AnnData.concatenate generates -inf values #544

Open lisa-sousa opened 3 years ago

lisa-sousa commented 3 years ago

I'm using anndata to store some facs data. After reading in the files (each file one sample) and storing the values in anndata format, I concatenate all the samples with ann.AnnData.concatenate(*anndata_sample_training). However, after concatenation, there are some -inf values introduced to the X data matrix. I checked the data before and after concatenation and before I have no -inf values but after concatenation I suddenly have around 30 -inf values in my dataset (values stored in X).

ivirshup commented 3 years ago

I haven't been able to reproduce this behaviour locally. Could you provide a minimal reproducible example of this? Something like what's described here. Information on what versions of packages you are using would be helpful too (like the output of sinfo.sinfo(dependencies=True)).