Retroviral lineage studies have been widely used over the past decade to study retinal development in vivo and in explant culture [Donovan S.L., Dyer, M.A., 2006. Preparation and Square Wave Electroporation of Retinal Explant Cultures, Nature Protocols 1, 2710-2718; Donovan, S.L., Schweers, B., Martins, R., Johnson D., Dyer, M.A., 2001. Compensation by tumor suppressor genes during retinal development in mice and humans, BMC Biol 4 , 14; Dyer M.A., Cepko, C.L., 2001. p27Kip1 and p57Kip2 regulate proliferation in distinct retinal progenitor cell populations, J. of Neurosci 21, 4259-4271; Dyer M.A., Cepko, C.L., 2000. p57(Kip2) regulates progenitor cell proliferation and amacrine interneuron development in the mouse retina, Development 127, 3593-3605; Dyer, M.A., Livesey, F.J., Cepko C.L., Oliver, G., 2003. Prox1 function controls progenitor cell proliferation and horizontal cell genesis in the mammalian retina, Nat Genet 34, 53-58]. These approaches can provide important data on the proliferation, cell fate specification, differentiation and survival of individual neurons and glia derived from single infected retinal progenitor cells. In some experiments, these parameters are compared in retinae from animals with different targeted deletions or transgenes. Alternatively, the effect of ectopic expression of virally encoded transgenes may be studied at the level of individual retinal progenitor cells in vivo and in explant culture. One of the challenges with interpreting retroviral lineage studies is determining the statistical significance of differences in the proliferation, cell fate specification, differentiation of survival of retinal progenitor cells between experimental and control samples. In this study, we provide a clear step-by-step guide to the application of statistical methods to retroviral lineage analyses actual data sets. We anticipate that this will serve as a guide for future statistical analyses of retroviral lineage studies and will help to provide a uniform standard in the field.