Genetic association studies using psychophysiology measures face many of the same problems as psychiatric genetic and behavior genetic research, including relatively small effect sizes of individual genes and complexity of phenotypes. Moreover, these problems are further exacerbated by such factors as lack of standardized assessments which hinders replication efforts and pooling data across laboratories, multiplicity of phenotype description (a single ERP experiment can generate a host of variables), and small sample sizes (because psychophysiology assessments require a lab visit). Clearly, the combination of multiple phenotypes, multiple genes, and small sample size is prone to produce false positive findings (Type I error). Apart from these general problems, there are a number of problems that are specific to the measurement of the phenotype and to certain aspects of the genetic analyses.
