When I export to h5ad from h5Seurat and my Seurat object has scaled data (for all genes), normalized data, and counts, the AnnData object .X has a number of genes equal to the number of highly variable genes, all of which are marked as highly variable in the AnnData object. But when I check the list of variable genes on the Seurat object and the gene names of the AnnData object, the two lists are not the same.
When I export to h5ad from h5Seurat and my Seurat object has scaled data (for all genes), normalized data, and counts, the AnnData object .X has a number of genes equal to the number of highly variable genes, all of which are marked as highly variable in the AnnData object. But when I check the list of variable genes on the Seurat object and the gene names of the AnnData object, the two lists are not the same.