chanzuckerberg/cellxgene

[BUG] Seurat v3 objects missing "key" in assays

zdebruine opened this issue · 4 comments

zdebruine commented

See satijalab/seurat#6408.

You may want to assign a value for the key in all @assays. This is causing issues with running Seurat functions "out of the box".

MaximilianLombardo commented

Thanks for flagging @zdebruine - I'll forward to the relevant team members!

brianraymor commented

Please see Use assay-specific naming for expression matrices in Seurat object which is pending.

Investigate missing data@assays$RNA@key in Seurat conversion has been addressed. All RDS datasets in the portal will be updated in October-November when we migrate to a new version of the cellxgene schema.

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MaximilianLombardo commented

@zdebruine This issue should no longer occur after the updates in October/November. Closing for now, but feel free to check back in or report your experience after the update.

zdebruine commented

@brianraymor @MaximilianLombardo Thanks all for this fast resolution! Looking forward to the updates in the next 1-2 months.

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