title: Matrix multiplication in pandas
body: <p>I have numeric data stored in two DataFrames x and y. The inner product from numpy works but the dot product from pandas does not.</p>
  
  <pre><code>In [63]: x.shape
  Out[63]: (1062, 36)
  
  In [64]: y.shape
  Out[64]: (36, 36)
  
  In [65]: np.inner(x, y).shape
  Out[65]: (1062L, 36L)
  
  In [66]: x.dot(y)
  ---------------------------------------------------------------------------
  ValueError                                Traceback (most recent call last)
  &lt;ipython-input-66-76c015be254b&gt; in &lt;module&gt;()
  ----&gt; 1 x.dot(y)
  
  C:\Programs\WinPython-64bit-2.7.3.3\python-2.7.3.amd64\lib\site-packages\pandas\core\frame.pyc in dot(self, other)
      888             if (len(common) &gt; len(self.columns) or
      889                     len(common) &gt; len(other.index)):
  --&gt; 890                 raise ValueError('matrices are not aligned')
      891 
      892             left = self.reindex(columns=common, copy=False)
  
  ValueError: matrices are not aligned
  </code></pre>
  
  <p>Is this a bug or am I using pandas wrong?</p>