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error:not a sparse matrix when converting h5ad to Seurat #176

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gmcregis opened this issue Mar 1, 2024 · 1 comment
Open

error:not a sparse matrix when converting h5ad to Seurat #176

gmcregis opened this issue Mar 1, 2024 · 1 comment

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@gmcregis
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gmcregis commented Mar 1, 2024

Convert("Trans_cis_cell_type_lablled.h5ad", dest = "h5seurat", overwrite = TRUE)
Warning: Unknown file type: h5ad
Warning: 'assay' not set, setting to 'RNA'
Creating h5Seurat file for version 3.1.5.9900
Adding X as data
Adding raw/X as counts
Adding meta.features from raw/var
Adding X_scVI as cell embeddings for scVI
Adding X_umap as cell embeddings for umap
Adding _scvi_extra_categorical_covs as cell embeddings for _scvi_extra_categorical_covs
Error: Not a sparse matrix

I've been getting the error above and looked through other issues but couldn't really find anything that worked for me; I tried editing the h5ad file in python but I'm not super familiar with it so if anyone can help I'd greatly appreciate it!

@AarronLi
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AarronLi commented Aug 9, 2024

have you ever sovled this problem? i also met the "Erro: Not a sparse matrix".

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