We have used a computer simulation to study properties of large-scale equatorial F region irregularities produced by gravity waves by separating such different processes as the spatial resonance effect and the Rayleigh-Taylor instability. Our purpose is to show their relative importance in the production of strong ionization perturbations. When a gravity wave propagates perpendicular to the magnetic field, it generates a polarization electric field. If there is no amplification by the Rayleigh-Taylor instability, the amplitude of the electric field remains almost constant for a long time. If spatial resonance occurs, after one wave period strong ionization perturbations with a relative density amplitude of 58% are produced. However, the associated electric field is limited and the gravity wave-induced perturbation does not grow into topside plasma bubbles when the Rayleigh-Taylor instability is absent. A zonally propagating gravity wave can, however, initiate the Rayleigh-Taylor instability in the bottomside F region. The initiation does not depend on the spatial resonance mechanism. After initiation, the Rayleigh-Taylor instability amplifies nonlinearly the perturbations induced by the seed gravity wave, and results in topside plasma bubbles. Spatial resonance can speed up the formation of bubbles. It is thus concluded that the Rayleigh-Taylor instability mechanism is the most important for production and rise of plasma bubbles and that seeding by gravity waves can occur even without the spatial resonance effect.