Exploration & description/ANOVA or REML?

Before using the REML method to estimate genetic variance components we shall rerun the analysis used in Case Study 3 to compare weaning weights of lambs. First we must disregard the lambs for which the response variable weaning weight was not recorded. This can be achieved by using the GenStat Spread → Restrict/Filter By Value... command and excluding missing values (*) for weaning weight

This time we shall alter the way that breed genotypes are defined in the least squares analysis. Instead of referring to the breeds by their genotype, D X D, D X R, R X D and R X R we shall consider separate effects for ram breed, ewe breed and their interaction, and re-parameterise the model accordingly. We can run this model both by least squares analysis of variance and by REML.

Let us first consider the least squares approach. Using Stats Regression Analysis Generalized Linear Models and completing the dialog box as shown and clicking the Options... button and then ticking 'Accumulated', we obtain the analysis of variance indicating that the breed of ram x breed of ewe is insignificant (variance ratio = 0.15).