Closed gouttegd closed 2 months ago
This issue was related to the issue #32. Before, I wasn't checking if there was already a cell_type to rename author_cell_type_ontology to cell_type. I fixed it. Can you double check it, please?
I just re-tested against E-MTAB-8698. The conversion ended without errors and the cell_type
column was populated correctly. Looks all good to me.
Thanks!
I ran into the following error when trying to process the E-MTAB-8698 dataset (one of the fly datasets):
This is during the RDF conversion step. The step that converts the SCXA H5AD file to the CxG scheme seemingly goes well (no error), but the resulting
…_modified.project.h5ad
file does not seem entirely correct. For example, there are twocell_type
columns in theobs
section (which I suspect might be the cause of the “Grouper for 'cell_type' not 1-dimensional” error above), as well as twocell_type_ontology_term_id
columns:And the contents of those columns seem bogus as well: