seurat-disk
seurat-disk copied to clipboard
error:not a sparse matrix when converting h5ad to Seurat
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!