Hi all, I'm reviewing a paper and ran into a mystery (hopefully not to you) trying to reproduce the stats. The authors uploaded their data to a repository. I've created a similar (though random) data set for confidentiality reasons. So the authors include one four-level treatment variable, but report results about the significance of the interaction, which seems incongruous. In the methods section, they also mention using Tukey's after ANOVA. I figured they might have included the treatment variable as a convenience to plot. Here, I split it into two new variables so I can create an interaction: So the authors mention lot was nested within the interaction. I thought that nesting would not have to be specified in the model explicitly, since R can tell whether, in this case, lots contain multiple treatment groups or whether there is no such replication. However, does not contain results for the interaction term (treat1:treat2) in the anova table. The following does work: Could anyone explain why the former doesn't work? BTW: the latter anova table is exactly the following as the following two. Curious also that, when you use the four-level treatment variable lot can be added as is or as an interaction term with the treatment variable only. This seems to be the flexibility that I expected R to have in the above model too. Any insights welcome! code.r <http://r.789695.n4.nabble.com/file/n4685011/code.r> -- View this message in context: http://r.789695.n4.nabble.com/model-specification-issue-tp4685011.html Sent from the R help mailing list archive at Nabble.com.