In investigations of shale gas found within shale formations, the conversion of the experimentally determined excess adsorption amount to the absolute amount is crucial to the interpretation of experimental adsorption data. In our study, the excess isotherms of a shale sample from the Longmaxi Formation in China are converted to absolute ones using existing methods. Keeping in mind that the results differ widely across methods and that the accuracies of these methods are poorly understood, we take a first step towards revealing and evaluating the possible discrepancies. We construct a molecular dynamics (MD) model considering methane adsorption in nanometer channels of different widths, and the model is able to calculate the excess and absolute adsorption amounts. Our simplified MD model is proved to be able to reproduce the excess adsorption isotherms of the shale sample through comparison with experimental data. We also evaluate existing conversion methods for calculation of the excess adsorption amount based on MD results. The methods that use predetermined adsorbedphase density values usually underestimate the absolute amount. Further, the modified Langmuir and Toth equation methods underestimate results under most conditions. The relative error is large at higher pressure, higher temperature, and in smaller channels, and it can be as large as 45%. Our study will serve to remind researchers about uncertainty of the results these methods, which can be useful in application.