I am struggling with a simple repeated-measure model: fit<-lme(trait~year * A, random = ~1|subj/year) A being a factor with three levels. I got have the following results for anova(fit): numDF denDF F-value p-value (Intercept) 1 126 2471.4720 <.0001 year 20 60 10.4126 <.0001 A 2 126 23.0721 <.0001 year:A 40 126 1.6499 0.0193 Now I try to use glht for A, but fail: Linear Hypotheses: Estimate Std. Error z value p value A2 - A1 == 0 0.25 1.10 0.227 0.972 A3 - A1 == 0 1.00 1.10 0.909 0.634 A3 - A2 == 0 0.75 1.10 0.682 0.774 (Adjusted p values reported -- single-step method) Warning message: In mcp2matrix(model, linfct = linfct) : covariate interactions found -- default contrast might be inappropriate What can be going on with this? many thanks in advance, Wolf