I have an anndata object (already normalized) that I subsetted using
adata_4 = adata_T[adata_T.obs['celltype'] == "CD4"]
The subsetting works but when I try to further process this data ie.
sc.pp.normalize_total(adata_4, inplace = True)
adata_4.layers['norm_counts'] = adata_4.X.copy()
adata_4.X = np.log2(adata_4.X + 1)
I get the error ‘coo_matrix’ object is not subscriptable