Alpha Level for Empirical LOD Thresholds

Specify an alpha level for computing comparison-wise and experiment-wise critical values for the LOD scores based on the permutation test statistics .

•	Comparison wise critical LOD values are computed at each QTL testing point by computing the 100(1- alpha )% percentile from the N LOD scores obtained from the permutation analysis (where N is the number of permutations performed).

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Experiment wise critical LOD thresholds are computed by finding the maximum LOD scores over all QTL testing points for each of the N permutation analyses. The 100(1- alpha )% percentile of these values for each trait is reported as the experimentwise critical LOD thresholds and are drawn on the LOD score plots.

Refer to Churchill and Doerge (Genetics, 1994) ¹ for additional information about this method.

Exact p-values for the LOD scores (calculated based on the empirical distribution ) are also reported using the alpha specified here as a reference significance threshold.

To Specify an Alpha Level:

Specify Haley-Knott Regression as the QTL Mapping Model Algorithm .

Type a value greater than or equal to 1 in the Number of Permutations to Compute field.

Type the alpha value into the Alpha Level for Empirical LOD Thresholds text field.

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1

Churchill, G.A., and R.W. Doerge. 1994. Empirical threshold values for quantitative trait mapping. Genetics 138:963-971.