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Background  By analyzing a "pseudo-trait," a trait not linked or associated with any of the markers tested, the distribution of the test statistic under the null hypothesis can provide the critical value for the appropriate percentile of the distribution. In addition, the anecdotal observation that  p -values tend to be more significant near the telomeres was investigated.    Results  The applied pseudo-trait (APT) method was applied to the Affymetrix and Illumina SNPs in the Collaborative Study on the Genetics of Alcoholism dataset to determine appropriate critical values for regression of offspring on mid-parent (ROMP) and Haseman-Elston association and linkage analyses, investigating the occurrence of type I errors in different chromosomal locations, and the extent to which the critical values obtained depend on the type of pseudo-trait used.    Conclusion  On average, the 5 percentile critical values obtained for this study were less than the expected 0.05. The distribution of  p -values does not seem to depend on chromosomal position for ROMP association analysis methods, but does in some cases for Haseman-Elston linkage analysis. Results vary with different pseudo-traits.

Critical values and variation in type I error along chromosomes in the COGA dataset using the applied pseudo-trait method