fix layer option seurat v3

dwnorton · Jul 29, 2020 · a4ad0a5 · a4ad0a5
1 parent b7c7130
commit a4ad0a5
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/scanpy/preprocessing/_highly_variable_genes.py b/scanpy/preprocessing/_highly_variable_genes.py
@@ -86,7 +86,7 @@ def _highly_variable_genes_seurat_v3(
         estimat_var[not_const] = model.outputs.fitted_values
         reg_std = np.sqrt(10 ** estimat_var)
 
-        batch_counts = adata[batch_info == b].X.astype(np.float64).copy()
+        batch_counts = X[batch_info == b].astype(np.float64).copy()
         # clip large values as in Seurat
         N = np.sum(batch_info == b)
         vmax = np.sqrt(N)