Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Exception: Some clusters/cell_types in microenvironments file are not present in metadata #184

Open
Jessica1525809 opened this issue Apr 25, 2024 · 3 comments

Comments

@Jessica1525809
Copy link

Jessica1525809 commented Apr 25, 2024

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.
截屏2024-04-25 23 40 14

Here are my codes:
截屏2024-04-25 23 42 59

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

@ktroule
Copy link
Collaborator

ktroule commented Apr 26, 2024

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
Copy link
Author

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
Copy link
Collaborator

ktroule commented Apr 30, 2024

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants