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Fixed all NANs when genes with all zeros. #11 #12

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Fixed all NANs when genes with all zeros. #11 #12

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802d39a
fixed NA output when input gene's values are all zeros
zqfang Dec 29, 2018
6dd3393
Merge remote-tracking branch 'upstream/master'
zqfang Dec 29, 2018
cc39bd7
improved
zqfang Dec 31, 2018
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3 changes: 3 additions & 0 deletions combat.py
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Expand Up @@ -84,6 +84,9 @@ def combat(data, batch, model=None, numerical_covariates=None):
for c in numerical_covariates if not c in drop_cols]

design = design_mat(model, numerical_covariates, batch_levels)
# remove genes with all zeros, if not, corrected dataframe will be all NAs.
sys.stderr.write("Preprocessing Data across genes.\n")
data = data[ (data != 0).sum(axis=1) > 0 ]

sys.stderr.write("Standardizing Data across genes.\n")
B_hat = np.dot(np.dot(la.inv(np.dot(design.T, design)), design.T), data.T)
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