I have less experience on writing protocols but I searched about this online and found that sample sizes are calculated based on the magnitude of effect that the researcher would like to see in his treatment population (compared with placebo). It is important to note variables such as prevalence, expected confidence level and expected treatment effect need to be predetermined in order to calculate sample size. As an example, Scarborough state that “on the basis of a background mortality of 56% and an ability to detect a 20% or greater difference in mortality, the initial sample size of 660 patients was modified to 420 patients to detect a 30% difference after publication of the results of a European trial that showed a relative risk of death of 0.59 for corticosteroid treatment.” Determining existing prevalence and effect size can be difficult in areas of research where such numbers are not readily available in the literature.