All,

I am testing an overall anova (4 groups; is there any difference across
groups) using the following design matrix in limma

  (Intercept) B C D
1           1 0 0 0
2           1 0 0 0
3           1 0 0 0
4           1 0 0 0
5           1 0 0 0
6           1 0 0 0

I have used ROAST (in limma) in the past with a specific contrast, such as

roast(expression_matrix,index,design_matrix,contrast=10,nrot=3000).

In the current case, I didn't need any contrasts. In limma, I had used

design <- model.matrix(~key$stage)
colnames(design)[2:4] = c("B","C","D")
fit <- lmFit(e, design)
fit <- eBayes(fit)
topTable(fit,adjust.method="BH")

to obtain the overall F-test (I understand this test is not that
interesting, but it is requested of me).

Using this setup, how can I specify this overall test within ROAST.

Thanks for your help.

Juliet

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