I'm assuming that a model which was fitted using the `Error()` function within `aov()` won't work when using in `plot()` because you will get more than one error stratum from which you can choose. Now you could use the `proj()` function which will give you the residuals for each error stratum in a way that allows you to extract them more easily. I found some information [here](http://stackoverflow.com/questions/26169153/how-to-get-residuals-from-repeated-measures-anova-model-in-r). **Edit 1 start** More information regarding multistratum models and the `proj()` function is given in Venables and Ripley, page 284 (but start from page 281): _Residuals in multistratum analyses: Projections_. In the second sentence they write (I highlighted in bold): >Thus `fitted(oats.aov[[4]])` and `resid(oats.aov[[4]])` are vectors of length 54 representing fitted values and residuals from the **last stratum**, based on 54 orthonormal linear functions of the original data vector. It is not possible to associate them uniquely with the plots of the original experiment. For your example that means: ex.aov.proj <- proj(ex.aov) # Check number of strata summary(ex.aov.proj) # Check for normality by using last error stratum qqnorm(ex.aov.proj[[9]][, "Residuals"]) # Check for heteroscedasticity by using last error stratum plot(ex.aov.proj[[9]][, "Residuals"]) However, this will also lead into plots which I cannot fully interpret (especially the second one). In their case, the last stratum was the `Within` stratum. Since your model cannot estimate this (presumably due to your error term), I am not sure if simply using your last stratum is valid. Hopefully someone else can clarify. **Edit 1 end** **Edit 2 start** According to [this source](http://www.personal.psu.edu/mar36/stat_461/split_plot/split_plot.html) checking residuals to assess normality and heteroscedasticity should be performed without the `Error()` function. >In order to check assumptions, you need to not use the error term. You can add the term without error, but the F tests are wrong. Assumption checking is OK, however. This seems reasonable to me but I hope someone else could clarify. **Edit 2 end** **My alternative suggestion:** First, I changed your dataset slightly and set a seed to make it reproducible (might be handy for some problems you have in the future): # Set seed to make it reproducible set.seed(12) # I changed the names of your variables to make them easier to remember # I also deleted a few nested `rep()` commands. Have a look at the `each=` argument. subj <- sort(factor(rep(1:20,8))) x1 <- rep(c('A','B'),80) x2 <- rep(c('A','B'),20,each=2) x3 <- rep(c('A','B'),10, each=4) outcome <- rnorm(80,10,2) d3 <- data.frame(outcome,subj,x1,x2,x3) Second, I used a linear mixed-effects model instead since you have repeated measures and hence a random term you can use: require(lme4) # I specified `subj` as random term to account for the repeated measurements on subject. m.lmer<-lmer(outcome ~ x1*x2*x3 + (1|subj), data = d3) summary(m.lmer) # Check for heteroscedasticity plot(m.lmer) [![enter image description here][1]][1] # or boxplot(residuals(m.lmer) ~ d3$x1 + d3$x2 + d3$x3) [![enter image description here][2]][2] # Check for normality qqnorm(residuals(m.lmer)) [![enter image description here][3]][3] Using the `afex` package you can also get the fixed effects in ANOVA table format (you can also use the `Anova()` function from the `car` package as another option): require(afex) mixed(outcome ~ x1*x2*x3 + (1|subj), data = d3, method="LRT") Fitting 8 (g)lmer() models: [........] Effect df Chisq p.value 1 x1 1 0.04 .84 2 x2 1 2.53 .11 3 x3 1 7.68 ** .006 4 x1:x2 1 8.34 ** .004 5 x1:x3 1 10.51 ** .001 6 x2:x3 1 0.31 .58 7 x1:x2:x3 1 0.12 .73 Check `?mixed` for the various options you can choose. Also regarding mixed models, there is a lot of information here on Cross Validated. [1]: https://i.sstatic.net/i1X6E.png [2]: https://i.sstatic.net/k58cP.png [3]: https://i.sstatic.net/R6PRH.png