**Author:** [@albi](https://discourse.scverse.org/u/albi)\
**Replies:** 6\
**Last updated:** [June 22, 2026, 11:49pm UTC](https://discourse.scverse.org/t/sd-filter-by-table-query-fails-with-indexerror-on-spatialdata-0-7-3-anndata-0-12-6/4012 "2026-06-22T23:49:11Z")
Hi, I’m encountering an IndexError when using sd.filter\_by\_table\_query() on a SpatialData object. Versions spatialdata: 0.7.3 anndata: 0.12.6 annsel: 0.1.2 Variables print(type(keep\_mask)) \>\ pri…
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## [How could \`adata.raw.X\` contain non-integer values?](https://discourse.scverse.org/t/how-could-adata-raw-x-contain-non-integer-values/3708)
**Author:** [@mschilli](https://discourse.scverse.org/u/mschilli)\
**Replies:** 2\
**Last updated:** [July 13, 2025, 7:56pm UTC](https://discourse.scverse.org/t/how-could-adata-raw-x-contain-non-integer-values/3708 "2025-07-13T19:56:26Z")
Hello scverse communtity, I need some help troubleshooting an issue I do not understand. I have a (non-public) H5ad file with a dataset that was analysed (QC, cell/gene/sample annotation, normalisation, dimensionality …
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## [Efficient pseudobulking](https://discourse.scverse.org/t/efficient-pseudobulking/3515)
**Author:** [@emdann](https://discourse.scverse.org/u/emdann)\
**Replies:** 4\
**Last updated:** [May 28, 2025, 12:08pm UTC](https://discourse.scverse.org/t/efficient-pseudobulking/3515 "2025-05-28T12:08:32Z")
With the newest anndata/scanpy releases, what is the recommended scverse workflow to pseudobulk efficiently a large anndata object? I.e. summing the counts for each var for groups of cells, based on some column in obs. I…
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## [How to appropriately transfer annotations from anndata to seurat](https://discourse.scverse.org/t/how-to-appropriately-transfer-annotations-from-anndata-to-seurat/3457)
**Author:** [@Slack90](https://discourse.scverse.org/u/Slack90)\
**Replies:** 2\
**Last updated:** [January 24, 2025, 11:44pm UTC](https://discourse.scverse.org/t/how-to-appropriately-transfer-annotations-from-anndata-to-seurat/3457 "2025-01-24T23:44:41Z")
Hi, I processed my rna seq data and annotated them using scvi, and I would like to integrate the data using R. Specifically, this is my anndata structure: AnnData object with n\_obs × n\_vars = 16712 × 10494 obs: 'se…
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## [How to convert R matrix to anndata](https://discourse.scverse.org/t/how-to-convert-r-matrix-to-anndata/3427)
**Author:** [@Slack90](https://discourse.scverse.org/u/Slack90)\
**Replies:** 4\
**Last updated:** [January 17, 2025, 8:27pm UTC](https://discourse.scverse.org/t/how-to-convert-r-matrix-to-anndata/3427 "2025-01-17T20:27:46Z")
Hi, I want to processed the raw RNAseq data deposited here in as “GSE165371\_cb\_adult\_mouse.tar.gz” GEO Accession viewer Here a screenshot of the folder content: As tiy can see it contains two text files and a .matr…
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## [NotImplementedError: Cannot create a view of an awkward array with \_\_array\_\_ parameter](https://discourse.scverse.org/t/notimplementederror-cannot-create-a-view-of-an-awkward-array-with-array-parameter/3305)
**Author:** [@yls2g13](https://discourse.scverse.org/u/yls2g13)\
**Replies:** 9\
**Last updated:** [November 6, 2024, 11:38am UTC](https://discourse.scverse.org/t/notimplementederror-cannot-create-a-view-of-an-awkward-array-with-array-parameter/3305 "2024-11-06T11:38:08Z")
Hi there, Thanks for these wonderful packages and scverse ecosystem. This is part 1/2 of an error I’m facing. I’m a Python and scverse beginner so I’m struggling to understand the error messages generated in Python - th…
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## [Anndata.concat(\[a,b\], join="inner") does not behave as a.concat(b)](https://discourse.scverse.org/t/anndata-concat-a-b-join-inner-does-not-behave-as-a-concat-b/2202)
**Author:** [@Fougere87](https://discourse.scverse.org/u/Fougere87)\
**Replies:** 1\
**Last updated:** [September 4, 2024, 4:31am UTC](https://discourse.scverse.org/t/anndata-concat-a-b-join-inner-does-not-behave-as-a-concat-b/2202 "2024-09-04T04:31:04Z")
Hi, I used to concatenate datasets to a reference one using the bound method a.concat(b). It was fairly handy because var were merged in an intersect fashion while obs were merged in an outer fashion, with NA added when…
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## [Does Scanpy stores raw count as int or float?](https://discourse.scverse.org/t/does-scanpy-stores-raw-count-as-int-or-float/2177)
**Author:** [@lwtan](https://discourse.scverse.org/u/lwtan)\
**Replies:** 1\
**Last updated:** [March 25, 2024, 8:30pm UTC](https://discourse.scverse.org/t/does-scanpy-stores-raw-count-as-int-or-float/2177 "2024-03-25T20:30:26Z")
Hi single-cell connoisseur, I am curious if the default type for AnnData raw object is float or int? For example: raw\_adata = adata.raw.to\_adata() raw\_adata.X Output: \<220752x29484 sparse matrix of type '\
**Author:** [@f6v](https://discourse.scverse.org/u/f6v)\
**Replies:** 2\
**Last updated:** [March 18, 2024, 10:46am UTC](https://discourse.scverse.org/t/normalized-data-found-instead-of-raw-counts/2163 "2024-03-18T10:46:24Z")
I’m running a scRNA-seq scVI workflow and getting warnings saying that non-integers were found in the AnnData: adata.layers\['counts'\] = adata.X.copy() sc.pp.normalize\_total(adata, target\_sum=1e4) sc.pp.log1p(adata) adat…
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## [Error with import scvi \_](https://discourse.scverse.org/t/error-with-import-scvi/1807)
**Author:** [@Marwansha](https://discourse.scverse.org/u/Marwansha)\
**Replies:** 1\
**Last updated:** [October 10, 2023, 1:49pm UTC](https://discourse.scverse.org/t/error-with-import-scvi/1807 "2023-10-10T13:49:03Z")
ImportError Traceback (most recent call last) Cell In\[6\], line 1 ----\> 1 import scvi File ~/anaconda3/scvi-env/lib/python3.10/site-packages/scvi/init.py:11 8 from .\_settings import set…
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## [Anndata 0.10 released!](https://discourse.scverse.org/t/anndata-0-10-released/1799)
**Author:** [@ivirshup](https://discourse.scverse.org/u/ivirshup)\
**Replies:** 0\
**Last updated:** [October 9, 2023, 10:50am UTC](https://discourse.scverse.org/t/anndata-0-10-released/1799 "2023-10-09T10:50:40Z")
anndata 0.10 has been released! You can check out the release notes here: Highlights from this release include: GPU support in AnnData via cupy dense and sparse arrays! You can take advantage of this right away with…