[BioC] What does maanova contrast?

[Loren Engrav]

Am using the maanova package 1.14.0

Model includes two breeds  (fixed breed factor) and 5 time points (random
time factor)

The three commands are

> BDeset_gcrma_NoCon25LRmadata.raw.WithAffyID081109 <-
read.madata("ABeset_gcrmaNoCon_25PsLRs081107.txt",
designfile="DesignV4LR081109.txt", header=TRUE, spotflag=FALSE, intensity=2,
probeid=1)

> BGanova.Br_T.mix081109 <-
fitmaanova(BDeset_gcrma_NoCon25LRmadata.raw.WithAffyID081109,
formula=~Breed+Time, random= ~Time, covariate = ~1, verbose=TRUE)

> ftest.Breed.mix_1000perm081109 <- matest
(BDeset_gcrma_NoCon25LRmadata.raw.WithAffyID081109, BGanova.Br_T.mix081109, term
= "Breed", n.perm = 1000, critical = .9, test.type = c("ftest"), shuffle.method
= c("sample"), MME.method = c("REML"), test.method = c(1,1), pval.pool = TRUE,
verbose = TRUE)

With two breeds and five time points there are 9 possible contrasts.  Does
the Ftest in maanova study all 9 breed contrasts or just the 5 breed
contrasts at the specific time points?

Thank you

-- 
Loren Engrav, MD
Univ Washington
Seattle