scikit-learn
diff --git a/‎sklearn/cross_validation.py‎
Lines changed: 4 additions & 2 deletions b/‎sklearn/cross_validation.py‎
Lines changed: 4 additions & 2 deletions
@@ -1756,8 +1756,10 @@ def _permutation_test_score(estimator, X, y, cv, scorer):
     """Auxiliary function for permutation_test_score"""
     avg_score = []
     for train, test in cv:
-        estimator.fit(X[train], y[train])
-        avg_score.append(scorer(estimator, X[test], y[test]))
+        X_train, y_train = _safe_split(estimator, X, y, train)
+        X_test, y_test  = _safe_split(estimator, X, y, test, train)
+        estimator.fit(X_train, y_train)
+        avg_score.append(scorer(estimator, X_test, y_test))
     return np.mean(avg_score)