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Pressure activity data as an important index of gastrointestinal (GI) motility can be obtained from the wireless radiotelemetry capsule. The Hilbert-Huang transform (HHT) method, which is more effective to process non-stationary signal, is proposed to identify the characteristics of GI motility. We decompose the pressure activity data into intrinsic mode functions (IMFs),calculate the Hilbert marginal spectrum and attain the peristalsis characteristics of GI tract. The IMFs represent the peristalses modes of GI tract activity embedded in the pressure data. The time-varying characteristic of the method suggests that the HHT is suitable to accommodate other non-stationary biomedical data analysis.