 <p>In general you should avoid performing multiple calls with <code>aov</code> and rather use a mixed effects linear model.</p> <p>You can find several examples in this <a href="http://blog.gribblelab.org/2009/03/09/repeated-measures-anova-using-r/" rel="nofollow">post by Paul Gribble</a></p> <p>I often use the <code>nlme</code> package, such as:</p> <pre><code>require(nlme) model &lt;- lme(dv ~ myfactor, random = ~1|subject/myfactor, data=mydata) </code></pre> <p>Depending on the situation you may run in more complex situations, I would suggest to have a look at the very clear book by Julian Faraway <em>"Extending the Linear Model with R: Generalized Linear, Mixed Effects and Nonparametric Regression Models"</em>.</p> <p>Also, you may want to ask on <a href="http://stats.stackexchange.com/">CrossValidated</a> if you have more specific statistical questions.</p>