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Hi @Pedramto89 the pvalue filter only adds NaN to the filtered values, but the interactions are still there in the output file. If you see a row/column filled with 0...

Hi @rachel662 could you please provide the command you used to launch `cellphonedb`? Additionally, It would be useful to know what versions of anndata/pandas/cellphonedb you're using. You can checked that...

> CellPhoneDB 2.1.6 > pandas 1.2.2 > anndata 0.7.5 That looks about right, could you please provide the command you used to launch `cellphonedb`?

It may be related to the encoding of your file. Could you try with this test meta and h5ad and see if you get the same error? [test_meta_and_count_h5ad.zip](https://github.com/Teichlab/cellphonedb/files/6038587/test_meta_and_count_h5ad.zip) That will...

Hi @rachel662 could you try upgrading to the beta version (`pip install -U CellPhoneDB==2.1.8b3`) and see if you're still facing this issue?

Hi @rachel662 meta should still be a .txt/csv/.tsv file. Is there any chance you could share your meta and counts files with us so we can have a better look...

> I tried this, however it didn't work, I think this might be because I haven't written the metadata file as a .h5ad file though? Hi @rachel662 not sure what...

Hi @mibo1996 could you please confirm which versions of cellphonedb and anndata are you using (`pip show cellphonedb anndata`)? I've tried reproducing this error but failed. Would you be able...

Thank you for the fast reply. I can see you're using v2.1.1 and h5ad support was introduced in version 2.1.6 I'd first recommend you try to update CellPhoneDB to the...

Hi @FionaMoon, thank you for using CellPhoneDB. Could you please let us know which version of R (`R --version`) and which version of rpy2 (`pip show rpy2`) do you have...