combat processing errors #1170
Description
...when I did combat batch correction, it outputs errors
# ComBat batch correction
sc.pp.combat(adata, key='sample')---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-5-350690ae55dc> in <module>
1 # ComBat batch correction
----> 2 sc.pp.combat(adata, key='sample')
~/anaconda2/envs/scanpy/lib/python3.6/site-packages/scanpy/preprocessing/_combat.py in combat(adata, key, covariates, inplace)
266 denom = np.dot(dsq, np.ones((1, n_batches[j])))
267 numer = np.array(bayesdata[batch_idxs] - np.dot(batch_design.loc[batch_idxs], gamma_star).T)
--> 268 bayesdata[batch_idxs] = numer / denom
269
270 vpsq = np.sqrt(var_pooled).reshape((len(var_pooled), 1))
ValueError: operands could not be broadcast together with shapes (23259,18243) (23259,15479) Versions:
scanpy==1.4.6 anndata==0.7.1 umap==0.3.10 numpy==1.17.3 scipy==1.3.1 pandas==0.25.2 scikit-learn==0.21.3 statsmodels==0.11.1 python-igraph==0.8.0