I am trying to get a handle on using maanova. I've managed to get everything sorted up to the point of running matest. I've seen the particular problem I will describe posted here before and there's never been a satisfactory solution that I can see. model.mixed.2 <- makeModel(data=myData.norm, formula=~Array+Dye+Treatment+Sample +Array:Sample+Array:Treatment, random=~Array) anova.mix.2<-fitmaanova(myData.norm, model.mixed.2) test.Treatment<-matest(myData.glowess, model=model.mixed.2,term="Treatment",n.perm=100) dies with: Error in var(log(Chis)) : missing observations in cov/cor In addition: Warning message: NAs produced in: rchisq(n, df) I've gone over my data and I don't see any missing values. I had a look at the primary maanova source code and don't see where this error is generated, so I am a bit stuck. Any advice?