I have firing-rate data for neurons ranging from 40-60 in number for various experimental groups. I've seen both mean and median being used in the literature, but without much explanation for the choice. My boss thinks that usually for sample sizes > 4-5, mean is ok to use. But I would like to have a better justification for my choice since the results I get with the two quantities are quite different.
Rather than compare means/medians why not fit a model to each and compare the distributions of parameter estimates for each group? This approach would seem to provide much more information.
Edit: I moved my "answer" to this question as it seemed somewhat offtopic here. How to fit this neuron firing model with R?