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The purpose of this study was to investigate students’ cognitive presence when online discussion was supported by scripted peer-facilitation. A total of 731 messages were analyzed. Analytic methods included both qualitative and quantitative content analysis. Bayesian approach of quantitative analysis was conducted to address the issues of using Null Hypothesis Significance Testing (NHST) for discussion data. Results showed that the scripted peer-facilitation was effective in creating and developing students’ cognitive presence, especially the cognitive presence of Triggering Event and Exploration.