In this study we assess the interchangeability and statistical agreement of two prevalent instruments from the non-invasive “sniffer” method and compare their precision. Furthermore, we develop and validate an effective algorithm for aligning time series data from multiple instruments to remove the effects of variable and fixed time shifts from the instrument comparison. The CH4 and CO2 gas concentrations for both instruments were found to differ for population means (P <0.05) and intra-cow variation (precision) (P <0.05) and for inter-cow variation (P <0.05). The CH4 and CO2 gas concentrations from both instruments can be used interchangeably to increase statistical power for example, in genetic evaluations, provided sources of disagreement are corrected through calibration and standardisation. Additionally, averaging readings of cows over a longer period of time (one week) is an effective noise reduction technique which provides phenotypes with considerable inter-cow variation. 
Interchangeability between methane measurements in dairy cows assessed by comparing precision and agreement of two non-invasive infrared methods