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The Wald test is inferior to the others regarding the accuracy of nominal significance levels.
Nominal significance level was set to p<0.05.
Our results showed that type 1 error rates were close to the nominal significance levels.
Seven of the 120 bins reached nominal significance in the schizophrenia analysis.
Loci meeting nominal significance criteria were interrogated for superimposed effects of other background loci (composite mapping).
Six of 120 bins on 4 chromosomes reached nominal significance in the bipolar GSMA analysis, under one or both models.
Loci meeting nominal significance criteria were interrogated for superimposed effects from other background loci (composite interval mapping).
However, several associations of nominal significance were detected concerning susceptibility to ACPA-negative RA and disease activity measures (DAS28).
Previously associated SNPs in EDN1, IL13, IL4R and TNF replicated at a nominal significance level between 0.05≥p>0.0035.
We now report the results of our exploratory analysis using a nominal significance level p<0.005 for unconditional tests.
At the same time, adjustment for population stratification can decrease the necessary level of nominal significance even further.
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