-
Notifications
You must be signed in to change notification settings - Fork 12
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
pandas.errors.InvalidIndexError: Reindexing only valid with uniquely valued Index objects #171
Comments
I posted about a similar issue. The work around of that was omitting |
Could this be due to the pandas 2.0? |
I think that the tuto isn't clear for that part. But i was able to move forward by adding the metadata to the individual cystopic object and only then merge it. |
Can you share the code how you did it? |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Describe the bug
After creating the citopic objects for each samples and merge it, i want to use the function cistopic_obj.add_cell_data(cell_data, split_pattern='-').
I get an error saying "Reindexing only valid with uniquely valued Index objects".
But there is no duplicated index in my cell data annotation. when I did the pre processing of the scRNA seq part I used:
matrix.obs_names_make_unique()
and also try to add :
matrix.obs_names = [f"{idx}_{sample}" for idx in matrix.obs_names]
before to concat all the samples together to create the object I used go clusterize and generate the cell data annotation.
I don't see where that error could come from ?
To Reproduce
Error output
The text was updated successfully, but these errors were encountered: