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The first example ¨Correcting from Numpy Array as Data¨ works smoothly,
but the second example ¨Correcting from pandas.DataFrame as Data¨ fails with the following error of shape not aligned, unless you feed neuroCombat with data.T in stead of data.
/neuroCombat/neuroCombat/neuroCombat.py in neuroCombat(data, covars, batch_col, discrete_cols, continuous_cols)
97 # standardize data across features
98 print('Standardizing data across features..')
---> 99 s_data, s_mean, v_pool = standardize_across_features(data, design, info_dict)
100
101 # fit L/S models and find priors
<array_function internals> in dot(*args, **kwargs)
ValueError: shapes (8,57) and (22283,57) not aligned: 57 (dim 1) != 22283 (dim 0)
The text was updated successfully, but these errors were encountered:
FinLouarn
changed the title
Example ¨Correcting from pandas.DataFrame as Data¨ need a data transpose
Example ¨Correcting from pandas.DataFrame as Data¨ needs a data transpose not to fail with shape not aligned
Jun 26, 2020
The first example ¨Correcting from Numpy Array as Data¨ works smoothly,
but the second example ¨Correcting from pandas.DataFrame as Data¨ fails with the following error of shape not aligned, unless you feed neuroCombat with data.T in stead of data.
python 3.7.7
pandas 0.25.3
ValueError Traceback (most recent call last)
in
15 batch_col=batch_col,
16 discrete_cols=discrete_cols,
---> 17 continuous_cols=continuous_cols)
/neuroCombat/neuroCombat/neuroCombat.py in neuroCombat(data, covars, batch_col, discrete_cols, continuous_cols)
97 # standardize data across features
98 print('Standardizing data across features..')
---> 99 s_data, s_mean, v_pool = standardize_across_features(data, design, info_dict)
100
101 # fit L/S models and find priors
/neuroCombat/neuroCombat/neuroCombat.py in standardize_across_features(X, design, info_dict)
159 sample_per_batch = info_dict['sample_per_batch']
160
--> 161 B_hat = np.dot(np.dot(la.inv(np.dot(design.T, design)), design.T), X.T)
162 grand_mean = np.dot((sample_per_batch/ float(n_sample)).T, B_hat[:n_batch,:])
163 var_pooled = np.dot(((X - np.dot(design, B_hat).T)**2), np.ones((n_sample, 1)) / float(n_sample))
<array_function internals> in dot(*args, **kwargs)
ValueError: shapes (8,57) and (22283,57) not aligned: 57 (dim 1) != 22283 (dim 0)
The text was updated successfully, but these errors were encountered: