diff --git a/doc/library/tensor/basic.rst b/doc/library/tensor/basic.rst
index 4d3a5736a7..fe9750bd2c 100644
--- a/doc/library/tensor/basic.rst
+++ b/doc/library/tensor/basic.rst
@@ -1144,9 +1144,9 @@ Indexing
 
 Like NumPy, PyTensor distinguishes between *basic* and *advanced* indexing.
 PyTensor fully supports basic indexing
-(see `NumPy's indexing  <http://docs.scipy.org/doc/numpy/reference/arrays.indexing.html>`_)
+(see `NumPy's indexing  <https://numpy.org/doc/stable/user/basics.indexing.html>`_)
 and `integer advanced indexing
-<http://docs.scipy.org/doc/numpy/reference/arrays.indexing.html#integer>`_.
+<https://numpy.org/doc/stable/user/basics.indexing.html#integer-array-indexing>`_.
 
 Index-assignment is *not* supported.  If you want to do something like ``a[5]
 = b`` or ``a[5]+=b``, see :func:`pytensor.tensor.subtensor.set_subtensor` and
diff --git a/pytensor/tensor/subtensor.py b/pytensor/tensor/subtensor.py
index 99ae67af9b..6c881a0312 100644
--- a/pytensor/tensor/subtensor.py
+++ b/pytensor/tensor/subtensor.py
@@ -1453,10 +1453,16 @@ def set_subtensor(x, y, inplace=False, tolerate_inplace_aliasing=False):
 
     Examples
     --------
-    To replicate the numpy expression "r[10:] = 5", type
-    >>> from pytensor.tensor import vector
-    >>> r = vector("r")
-    >>> new_r = set_subtensor(r[10:], 5)
+    To replicate the numpy expression ``r[10:] = 5``, type
+
+    .. code-block:: python
+
+        from pytensor.tensor import set_subtensor, vector
+
+        r = vector("r")
+        new_r = set_subtensor(r[10:], 5)
+
+    Consider using :meth:`pytensor.tensor.variable.TensorVariable.set` instead.
 
     """
     return inc_subtensor(
@@ -1504,17 +1510,21 @@ def inc_subtensor(
     --------
     To replicate the expression ``r[10:] += 5``:
 
-    ..code-block:: python
+    .. code-block:: python
+
+        from pytensor.tensor import ivector, inc_subtensor
 
-        r = ivector()
+        r = ivector("r")
         new_r = inc_subtensor(r[10:], 5)
 
     To replicate the expression ``r[[0, 1, 0]] += 5``:
 
-    ..code-block:: python
+    .. code-block:: python
+
+        r = ivector("r")
+        new_r = inc_subtensor(r[[0, 1, 0]], 5, ignore_duplicates=True)
 
-        r = ivector()
-        new_r = inc_subtensor(r[10:], 5, ignore_duplicates=True)
+    Consider using :meth:`pytensor.tensor.variable.TensorVariable.inc` instead.
 
     """
     # First of all, y cannot have a higher dimension than x,