Exception: Some clusters/cell_types in microenvironments file are not present in metadata

[Jessica1525809]

Hi @ktroule ,
When I run cpdb_statistical_analysis_method.call with microenvironments file, the error arose: Exception: Some clusters/cell_types in microenvironments file are not present in metadata.

But I checked my metadata file and microenvironments file, their cell_types were consistent.

Here are my codes:

Thank you very much if you can solve my problem kindly!

[ktroule]

Hi.

Only thing that comes to mind right now its that one of the input files is not correctly formatted, check this.

Examples of files can be found here.

Kind regards.

[Jessica1525809]

Hi @ktroule,
I checked my files again but failed to find any problems. I think my files match the requirements.
Here are my metadata file and microenvironments file.
AllCategory_microenv.csv
AllCategory_meta.csv
Could you please check them for me？
Thanks a lot!
Best regards.

[ktroule]

Your files contain rows indices, the files should look like this:
microenvironments.tsv

cell_type	microenvironment
PV MMP11	Env1
PV MYH11	Env1
PV STEAP4	Env1

metadata.tsv

barcode_sample	cell_type
AGCGATTAGTCTAACC-1_Pla_HDBR10917733	B_cells
ATCCGTGAGGCTAGAA-1_Pla_Camb10714918	B_cells
AGTAACCCATTAAAGG-1_Pla_HDBR10917733	B_cells
GTTCACCTCAATGAGG-1_Pla_HDBR10142864	B_cells

Regards