[BioC] Commands with maanova

[Loren Engrav]

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.