am doing mixed linear regression with the maanova package the design file has six columns Array which is the number of the array Dye where all are 1 Sample ranging from 1 to 30 Breed either Duroc or Yorkshire PigID simply the number of the pig Time either 1 2 3 12 or 20 weeks and the difference of interest is breed over time the three commands are > file2 <- read.madata("file1.txt", designfile="DesignV4LR081109.txt", header=TRUE, spotflag=FALSE, intensity=2, probeid=1) > file3 <- fitmaanova(file2, formula=~Breed+Time, random= ~Time, covariate = ~1, verbose=TRUE) > file4 <- matest (file2, file3, term = "Breed", n.perm = 1000, critical = .9, test.type = c("ftest"), shuffle.method = c("sample"), MME.method = c("REML"), test.method = c(1,0,1,1), pval.pool = TRUE, verbose = TRUE) Have I missed anything? Or done anything wrong? Thank you.