Windows QTL Cartographer 2.5 - FTP Directory Listing

© 2010 N.C. State University, Bioinformatics Research Center
WinQTLCart Procedures 57
values for each trait. Select a different trait number to see the threshold value of that trait.
3. Select whether you want to set the threshold levels manually or have WinQTLCart determine the
threshold via permutations.
If you... Do this... Comments
Know the threshold values you
want to use
Don't know the threshold values
you want to use
Setting threshold levels manually
Input them into the Manual Input
57 box
Select By Permutations 57
to have
WinQTLCart calculate them.
This analysis occurs before you start the QTL analysis.
Permutations take a long time to
run. If 1 permutation runs for 10
seconds, than 1000 permutations
will take 2-3 hours.
Use this procedure to set the threshold for each trait manually. This is useful if you know the value for
each trait. Alternatively, select All Traits and apply this threshold setting to all the traits.
1. From the Trait Selection pull-down, select a trait to find the threshold value for that trait. (The All
Traits selection is available for permutations only.)
2. Click the By Manual Input option.
3. Input a threshold value into the box.
4. Optional: Click Set as Default if you want to assign the threshold value you entered to all traits.
Setting threshold levels via permutations
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.