diff --git a/combat/pycombat.py b/combat/pycombat.py index 8f01dda..650f26f 100644 --- a/combat/pycombat.py +++ b/combat/pycombat.py @@ -88,7 +88,7 @@ def compute_prior(prior, gamma_hat, mean_only): if mean_only: return 1 m = np.mean(gamma_hat) - s2 = np.var(gamma_hat) + s2 = np.var(gamma_hat, ddof=1) if prior == 'a': return (2*s2+m*m)/s2 elif prior == 'b': @@ -521,11 +521,11 @@ def fit_model(design, n_batch, s_data, batches, mean_only, par_prior, precision, else: for i in batches: # feed incrementally delta_hat list_map = np.transpose(np.transpose(s_data)[i]).var( - axis=1) # variance for each row + axis=1, ddof=1) # variance for each row delta_hat.append(np.squeeze(np.asarray(list_map))) gamma_bar = list(map(np.mean, gamma_hat)) # vector of means for gamma_hat - t2 = list(map(np.var, gamma_hat)) # vector of variances for gamma_hat + t2 = gamma_hat.var(axis=1, ddof=1).flatten().tolist()[0] # vector of variances for gamma_hat # calculates hyper priors for gamma (additive batch effect) a_prior = list(