Examples with many covariates

[olgabot]

Even after reading the code, I'm still confused about how to run this program with multiple covariates.

I thought I could do:

design = patsy.dmatrix('~ RIN + Index', metadata_expanded, return_type='dataframe')
combat(study.expression.data, ['RIN', 'Index'], design, numerical_covariates=['RIN'])

But I get this error (I copied the contents of combat.py to the flotilla package)

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-96-49a3d6446dc7> in <module>()
----> 1 combat(study.expression.data, ['RIN'], design, numerical_covariates=['RIN'])

/home/obotvinnik/workspace-git/flotilla/flotilla/external/combat.py in combat(data, batch, model, numerical_covariates)
     67 
     68     if model is not None and isinstance(model, pd.DataFrame):
---> 69         model["batch"] = list(batch)
     70     else:
     71         model = pd.DataFrame({'batch': batch})

/home/obotvinnik/anaconda/lib/python2.7/site-packages/pandas/core/frame.pyc in __setitem__(self, key, value)
   2108         else:
   2109             # set column
-> 2110             self._set_item(key, value)
   2111 
   2112     def _setitem_slice(self, key, value):

/home/obotvinnik/anaconda/lib/python2.7/site-packages/pandas/core/frame.pyc in _set_item(self, key, value)
   2185 
   2186         self._ensure_valid_index(value)
-> 2187         value = self._sanitize_column(key, value)
   2188         NDFrame._set_item(self, key, value)
   2189 

/home/obotvinnik/anaconda/lib/python2.7/site-packages/pandas/core/frame.pyc in _sanitize_column(self, key, value)
   2258         elif (isinstance(value, Index) or is_sequence(value)):
   2259             from pandas.core.series import _sanitize_index
-> 2260             value = _sanitize_index(value, self.index, copy=False)
   2261             if not isinstance(value, (np.ndarray, Index)):
   2262                 if isinstance(value, list) and len(value) > 0:

/home/obotvinnik/anaconda/lib/python2.7/site-packages/pandas/core/series.pyc in _sanitize_index(data, index, copy)
   2543 
   2544     if len(data) != len(index):
-> 2545         raise ValueError('Length of values does not match length of '
   2546                          'index')
   2547 

ValueError: Length of values does not match length of index