Abstract
In planning a study, the choice of sample size may depend on a variance value based on speculation or obtained from an earlier study. Scientists may wish to use an internal pilot design to protect themselves against an incorrect choice of variance. Such a design involves collecting a portion of the originally planned sample and using it to produce a new variance estimate. This leads to a new power analysis and increasing or decreasing sample size. For any general linear univariate model, with fixed predictors and Gaussian errors, we prove that the uncorrected fixed sample F-statistic is the likelihood ratio test statistic. However, the statistic does not follow an F distribution. Ignoring the discrepancy may inflate test size. We derive and evaluate properties of the components of the likelihood ratio test statistic in order to characterize and quantify the bias. Most notably, the fixed sample size variance estimate becomes biased downward. The bias may inflate test size for any hypothesis test, even if the parameter being tested was not involved in the sample size re-estimation. Furthermore, using fixed sample size methods may create biased confidence intervals for secondary parameters and the variance estimate.