Category » Controlling for False-Positives

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1. What is the difference between single and full scan permutations?
   These permutations are accessed from the Genetic Association Tests Window. For this example, let’s assume we have 50 markers and run 100 permutations. Of course, these are user defined. With a single scan permutation: 1. For each of the 50 markers, we run 100 permutations on our dependent var ...
2. How does permutation testing work in the Regression Module?
   The permutation of p-values in the regression module will permute the p-value for the overall haplotype trend regression (HTR) test x-number of times. The permutation changes the order of the dependant variable randomly, then runs HTR test again doing the moving window computation on all SNPs. A ...