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mojaveazure / seurat-disk

Interfaces for HDF5-based Single Cell File Formats
https://mojaveazure.github.io/seurat-disk
GNU General Public License v3.0
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error:not a sparse matrix when converting h5ad to Seurat #176

Open gmcregis opened 9 months ago

gmcregis commented 9 months ago

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 commented 3 months ago

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