We recently reported a new measurement of the electron's electric dipole moment using YbF molecules [Nature 473, 493 (2011)]. Here, we give a more detailed description of the methods used to make this measurement, along with a fuller analysis of the data. We show how our methods isolate the electric dipole moment from imperfections in the experiment that might mimic it. We describe the systematic errors that we discovered, and the small corrections that we made to account for these. By making a set of additional measurements with greatly exaggerated experimental imperfections, we find upper bounds on possible uncorrected systematic errors which we use to determine the systematic uncertainty in the measurement. We also calculate the size of some systematic effects that have been important in previous electric dipole moment measurements, such as the motional magnetic field effect and the geometric phase, and show them to be negligibly small in the present experiment. Our result is consistent with an electric dipole moment of zero, so we provide upper bounds to its size at various confidence levels. Finally, we review the prospects for future improvements in the precision of the experiment. ; Comment: 35 pages, 15 figures