ValueError: operands could not be broadcast together with shapes while using two sample independent t test
The answer to this question would be :
The objects created by the xs method of the Pandas DataFrame look like two-dimensional arrays. These must be flattened to look like one-dimensional arrays when passed to ttest_ind. The values attribute of the Pandas objects gives a numpy array, and the ravel() method flattens the array to one-dimension. 
It would go like : 

df  = pd.read_csv('final_out_transposed.csv', header=[1,2], index_col=[0])
case = df.xs('0', axis=1, level=0).dropna()
ctrl = df.xs('1', axis=1, level=0).dropna()
(tt_val,p_ttest ) = ttest_ind(case.values.ravel(), ctrl.values.ravel(), 
equal_var=False)
print (tt_val)
print(p_ttest)