The
Scree Plot
tab displays a plot of the
eigenvalue
for the ith component versus i to show the proportion of variation explained by the
principal components
. This tab is generated when the
Display principal components plots
check box has been checked
A
scree plot
can be useful in determining how many principal components to include in the
model
testing for
association
. Often the component where the plot begins to flatten out is the best choice for the number of components to use. This process can be run first without any
Trait Variables
specified and a large number for the
Maximum Number of Principal Components
specified. The Scree Plot can then be used to determine how many PCs to use for the association testing. The process can then be re-run with the PCA data set filled in and the Maximum Number of Principal Components set to the number chosen from the scree plot.