INNER CODE UNIT · Python

sizeFactor

scverse/PyDESeq2 · src/pydeseq2/dds.py:627

            def sizeFactor(x):
                _mask = np.logical_and(_control_mask, x > 0)
                return np.exp(np.median(np.log(x[_mask]) - logmeans[_mask]))

            sf = np.apply_along_axis(sizeFactor, 1, self.X)
            del log_counts

            # Normalize size factors to a geometric mean of 1 to match DESeq
            self.obs["size_factors"] = sf / (np.exp(np.mean(np.log(sf))))
            self.layers["normed_counts"] = (
                self.X / self.obs["size_factors"].to_numpy()[:, None]
            )
            self.logmeans = logmeans

        # Test whether it is possible to use median-of-ratios.
        elif (self.X == 0).any(0).all():
            # There is at least a zero for each gene
            warnings.warn(

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