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Error loading in UMAP layer

See original GitHub issue

Hi there,

I am trying to create an h5ad file from a raw expression matrix, a metadata file and UMAP coordinates. I’m getting the following error loading in anndata.obsm[‘X_umap’]:

ValueError: value.index does not match parent’s axis 0 names

the index values for the UMAP tsv and the metadata file used to create .obs are exactly the same, so i’m not sure what’s causing this. I did run .var_names_make unique on the matrix, but from my understanding that doesn’t apply to the index column. let me know if anyone can help!

Issue Analytics

State:
Created 2 years ago
Comments:7 (5 by maintainers)

Top GitHub Comments

5reactions

ivirshupcommented, Mar 31, 2021

I think this has actually been fixed on master, but not in a release yet. I could reproduce @rachadele’s error with 0.7.5, but not with the dev version.

This package could definitely use a bugfix release, so I’m aiming to do that over the long weekend.

0reactions

ivirshupcommented, Mar 31, 2021

Fixed in #461

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