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Type I error concentric circles
Previous: Screening for relevant markers.
GGEbiplot now is ready to generate the marker by environment biplot. Before that, it will ask if you want to add a set of type I error threshold circles on the biplot, which can serve as an experiment-wise error control:
If you select 'No', GGEbiplot will just generate and display the marker by environment biplot. If the selection is "Yes', you will be asked for the number of permutations to generate the threshold circles:
GGEbiplot remembers previous permutations, and will ask if you want to use existing permutation results or to do it over again:
When permutation is complete, GGEbiplot will ask for a probability level of the threshold circles.
The following biplot is a marker-effect by environment biplot with concentric circles of 0.05:
Note that there are five concentric circles, labeled as 0.05--, 0.05-, 0.05, 0.05+, and 0.05++. This gives a range of 5% type I error. A range is needed as the biplot is not an exact display of the marker-by-environment two-way table. You can choose the least stringent (inner most circle) or the most stringent circle (the outer most circle) to delete markers with short vectors (small effects). There should be no major difference in the identification of QTL; any difference is only about the inclusion or exclusion of minor QTL. We here remove all markers based on the most stringent circle:
Next: Determining the number of QTL.