** Next:** REFERENCES
** Up:** ZMAPQTL
** Previous:** MODELS
** Contents**
** Index**

##

PERMUTATION TESTS

Churchill and Doerge (1994) describe a method to calculate the threshold
values for quantitative trait mapping that we have implemented in this
program. Basically, it does a permutation of the trait values and the
genotypes and redoes the analysis. Over the number of replicates, two
types of thresholds are defined: "experimentwise" and "comparisonwise".
We calculate the experimentwise thresholds, but only give p values
for the comparisonwise values to save on storage space. The p values
give the proportion of permuted replicates that have loglikelihood
ratios larger than the observed ratios.

If you choose to do permutation tests, you need to run **Zmapqtl**
with the model of choice prior to doing the permutation test. Also, if
the program terminates prematurely, you can restart it from where it left
off to complete the permutation test.

Christopher Basten
2002-03-27