The analysis of variance

M. Drew LaMar
April 6, 2016

Class announcements

  • Exam #2 graded!
  • Exam #3 is on Friday, April 22.

Exam #2

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
  48.61   69.44   79.17   78.12   87.50   97.22       1 

Exam #2

boxplot(grades$Exam2, datax=TRUE)

plot of chunk unnamed-chunk-4

Permutation tests

Definition: A permutation test generates a null distribution for the association between two variables by repeatedly and randomly rearranging the values of one of the two variables in the data.

This is a form of bootstrapping.

Permutation tests for association

In this chapter, we explore a permutation test replacement for the two-sample \( t \)-test.

Variations on this theme can be done for many other tests.

Permutation tests for association



Permutation tests


  • Choose a test statistic that measures association between the two variables in the data (e.g. \( \bar{Y}_{1}-\bar{Y}_{2} \); Why not \( t \)?)
  • Create a permuted sample of data in which the values of the response variables are randomly reordered.
  • Calculate the chosen test statistic for the permuted sample.
  • Repeat the permutation process many times – at least 1000 or more.
  • Compute the \( P \)-value by comparing the observed test statistic (from original data) to this bootstrapped null distribution.

Example: Autoimmune and gut microbes