Parameters | Genetics | Alpha Level for Empirical LOD Thresholds

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.
Comparisonwise 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).
Experimentwise 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 the alpha value into the Alpha Level for Empirical LOD Thresholds text field.

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