diff --git a/decoupler/utils_anndata.py b/decoupler/utils_anndata.py
index c759d6a..7979682 100644
--- a/decoupler/utils_anndata.py
+++ b/decoupler/utils_anndata.py
@@ -160,7 +160,7 @@ def format_psbulk_inputs(sample_col, groups_col, obs):
 
     if groups_col is None:
         # Filter extra columns in obs
-        cols = obs.groupby(sample_col, observed=True).nunique().eq(1).all(0)
+        cols = obs.groupby(sample_col, observed=True).nunique(dropna=False).eq(1).all(0)
         cols = np.hstack([sample_col, cols[cols].index])
         obs = obs.loc[:, cols]
 
@@ -179,7 +179,7 @@ def format_psbulk_inputs(sample_col, groups_col, obs):
             groups_col = joined_cols
 
         # Filter extra columns in obs
-        cols = obs.groupby([sample_col, groups_col], observed=True).nunique().eq(1).all(0)
+        cols = obs.groupby([sample_col, groups_col], observed=True).nunique(dropna=False).eq(1).all(0)
         cols = np.hstack([sample_col, groups_col, cols[cols].index])
         obs = obs.loc[:, cols]