Setting threshold levels via permutations

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This analysis occurs before you start the QTL analysis.

Setting values via permutations allows WinQTLCart to empirically estimate the genome-wide significance threshold. Use this procedure if you don't know the value and you want WinQTLCart to find the optimal threshold.

Threshold values will be filled in automatically for every trait according to significance level.

Following threshold analysis, WinQTLCart will display the results in the Data pane and save them in a text file. The text file's name is displayed in the form after the analysis completes.

1.	From the Trait Selection pull-down, do one of the following:

·

Select one trait to find the threshold value for that trait.

·

Select All Traits to find threshold values for all traits.

2.	Click the By Permutations option.

3.	Enter a value for Permutation Times to set the permutation repeating times.

Note

If you want a quick run, use the default value of 300. But if you're going to publish, use the 1000 value; this will take several hours to run but will yield very precise results. We recommend starting this analysis before you leave for the day and letting it run overnight.

4.    Enter a value for Significance Level.
5.    Click OK to begin threshold analysis.

Note	You cannot update the All Traits checkbox. WinQTLCart checks or clears this box based on whether you select one or all traits from the drop down list.

After you click OK, WinQTLCart displays a countdown showing its progress through the file. When the threshold analysis is complete, WinQTLCart will display the results in the Data pane and display the results file's name. (WinQTLCart saves the file to the current working directory.)

After setting the threshold value, move on to finish the IM or CIM analysis procedure.