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Patient-physician agreement was scored using the Kappa method.
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Most of the annotation sources do not have hierarchical structures like GO, so the tool uses the kappa method directly on the equally weighted flat matrix.
The new data was entered and analyzed to check the reliability using the Kappa coefficient method whenever appropriate.
Next, we calculated the agreement between investigator review and the other methods using the kappa statistic (11 ).
The intra-rater reproducibility of this method was evaluated using the kappa score to 0.90 (p < 0.0001).
The agreement of the different classification methods was calculated using the kappa statistic.
The agreement of the classification methods was calculated using the kappa statistic, and survival associated with group membership was evaluated using survival analysis.
Agreements between methods were calculated using the Kappa test for staining intensities (Tables S2 and 4), and OCCC for positive tumor ratios (Table 4).
Results from the comparison of the conventional PCR vs. real-time PCR were plotted in a 2 × 2 table, and the agreement between results from the two methods was assessed using the kappa statistic for concordance and McNemar's test for discordance [ 12].
Results from the comparison of the real-time PCR vs. culturing were plotted in a 2 × 2 table, and the agreement between results from the two methods was assessed using the kappa statistic for concordance and McNemar's test for discordance [ 12].
Hence, we developed a more efficient inference method for cause discovery using the Kappa index.
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