You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Ingest this as a SOMA using tiledbsoma.io.from_h5ad. Then outgest using tiledbsoma.io.to_h5ad. Resulting error:
tiledbsoma._exception.SOMAError: internal error: encountered non-rectangular varm[PCs]: 22068 does not divide 46200
For this dataset:
nobs is 32458
nvar is 22068
varm/PCs is 22038 tall (not 22068) x 30 wide
The to_h5ad is being unit-tested in the repo, but, for data wherein varm height matches nvar. We need to deep-dive what it means for this dataset for varm height to differ from nvar, and, if this is something that's not downright pathological about this particular dataset, find out how to handle it more elegantly.
A good solution here might benefit from the bounding-box-as-metadata topic discussed on #1445.
The text was updated successfully, but these errors were encountered:
johnkerl
changed the title
[python] Occasional mis-shaping issue for to_h5ad on varm/PCs
[python] Occasional mis-shaping issue for to_h5ad/to_anndata on varm/PCsAug 29, 2023
johnkerl
changed the title
[python] Occasional mis-shaping issue for to_h5ad/to_anndata on varm/PCs
[python] Occasional mis-shaping issue for to_h5ad/to_anndata on obsm/varmAug 30, 2023
Using the following dataset:
https://cellxgene.cziscience.com/collections/2b02dff7-e427-4cdc-96fb-c0f354c099aa
Ingest this as a SOMA using
tiledbsoma.io.from_h5ad
. Then outgest usingtiledbsoma.io.to_h5ad
. Resulting error:For this dataset:
nobs
is 32458nvar
is 22068varm/PCs
is 22038 tall (not 22068) x 30 wideThe
to_h5ad
is being unit-tested in the repo, but, for data whereinvarm
height matchesnvar
. We need to deep-dive what it means for this dataset forvarm
height to differ fromnvar
, and, if this is something that's not downright pathological about this particular dataset, find out how to handle it more elegantly.A good solution here might benefit from the bounding-box-as-metadata topic discussed on #1445.
The text was updated successfully, but these errors were encountered: