search

jsxlei / SCALE

Single-cell ATAC-seq analysis via Latent feature Extraction
MIT License
97 stars 17 forks source link

KeyError: 'imputed' or 'binary' using the new version of SCALE #27

Closed litxiaoyao closed 9 months ago

litxiaoyao commented 9 months ago

I have successfully runed --impute, and successfully got the adata.h5ad file. However, it cracked when calling adata.obsm['imputed'] image

jsxlei commented 9 months ago

It should have. You can use the latest version of SCALE and use option --binary. This should work. You can check the keys in adata.obsm to see if there is an 'impute' or 'binary' exist. Let me know if you have any question.

litxiaoyao commented 9 months ago

It should have. You can use the latest version of SCALE and use option --binary. This should work. You can check the keys in adata.obsm to see if there is an 'impute' or 'binary' exist. Let me know if you have any question.

Thanks for your reply, lei. I have installed SCALE by pip, and I have tried using --binary but it didn't work and retain the same as --impute. So should I reinstall SCALE using git clone?

jsxlei commented 9 months ago

Try this command to install: pip install git+https://github.com/jsxlei/SCALE.git

litxiaoyao commented 9 months ago

Thank you very much lei!! It works when using this version of SCALE and using --impute parameter rather than --binary to get both keys 'impute' or 'binary' in adata.obsm. Besides, the key name is 'impute' rather than 'imputed' in the README.md.