  In the near future galaxy surveys will target Lyman alpha emitting galaxies
(LAEs) to unveil the nature of the dark energy. It has been suggested that the
observability of LAEs is coupled to the large scale properties of the
intergalactic medium. Such coupling could introduce distortions into the
observed clustering of LAEs, adding a new potential difficulty to the
interpretation of upcoming surveys. We present a model of LAEs that
incorporates Lyman-alpha radiative transfer processes in the interstellar and
intergalactic medium. The model is implemented in the GALFORM semi-analytic
model of galaxy of formation and evolution. We find that the radiative transfer
inside galaxies produces selection effects over galaxy properties. In
particular, observed LAEs tend to have low metallicities and intermediate star
formation rates. At low redshift we find no evidence of a correlation between
the spatial distribution of LAEs and the intergalactic medium properties.
However, at high redshift the LAEs are linked to the line of sight velocity and
density gradient of the intergalactic medium. The strength of the coupling
depends on the outflow properties of the galaxies and redshift. This effect
modifies the clustering of LAEs on large scales, adding non linear features. In
particular, our model predicts modifications to the shape and position of the
baryon acoustic oscillation peak. This work highlights the importance of
including radiative transfer physics in the cosmological analysis of LAEs.
