diff --git a/src/openqdc/datasets/base.py b/src/openqdc/datasets/base.py
index 91a8482..5ad18d4 100644
--- a/src/openqdc/datasets/base.py
+++ b/src/openqdc/datasets/base.py
@@ -205,6 +205,8 @@ def _remove_outliers(
             f"{avg_fn} is not a valid option, should be one of {list(BaseDataset.avg_options.keys())}"
         )
         logger.info(f"Removing outliers outside {avg_fn} +/- {num_stds} stds")
+        formation_E /= self.data["n_atoms"] # convert to avg formation energy / atom
+        formation_E = np.squeeze(formation_E.T) # remove extra array dimension and transpose
         fn = BaseDataset.avg_options[avg_fn]
         mid = fn(formation_E)
         mask = np.logical_or(formation_E < mid - num_stds * formation_E.std(), formation_E > mid + num_stds * formation_E.std())
@@ -232,7 +234,7 @@ def _precompute_E(self):
 
         # remove outliers if requested in __init__
         if self.remove_outliers:
-            E = self._remove_outliers(np.squeeze(E.T),
+            E = self._remove_outliers(E,
                                       avg_fn=self.avg_fn,
                                       num_stds=self.num_stds)