a perplexing error while converting H5AD to a Seurat object. #182
Description
Dear authors or esteemed peers who may read this post,
Recently, I encountered the following error while processing H5AD format data using seurat-disk:
Convert('SEVtras_combined.h5ad', "h5seurat", overwrite = TRUE, assay = "RNA")
Warning: Unknown file type: h5ad
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_pca as cell embeddings for pca
Adding X_umap as cell embeddings for umap
Adding PCs as feature loadings for pca
Warning: Cannot find features for feature loadings, will not be able to load
Adding miscellaneous information for pca
Adding standard deviations for pca
Adding miscellaneous information for umap
Adding hvg to miscellaneous data
Adding log1p to miscellaneous data
seurat_obj <- LoadH5Seurat("SEVtras_combined.h5seurat")
Validating h5Seurat file
Initializing RNA with data
Error in fixupDN.if.valid(value, x@Dim) :
length of Dimnames[[1]] (21203) is not equal to Dim[1] (4542)
The H5AD file that needs conversion originates from my own data, but I am unsure about the specific error that occurred during my data processing. I would greatly appreciate any advice or insights from you or any experienced individuals who have encountered and resolved this issue before. Thank you very much!