[BioC] limma design matrix with common reference

[Ron Ophir]

Hi,
I am analyze two color experiment with a common reference. It is a two
factor experiment with the following targets :
Cy3	Cy5
IE	Control
IL	Control
EE	Control
EL	Control
IE	Control
IL	Control
EE	Control
EL	Control
IE	Control
IL	Control
EE	Control
EL	Control
IE	Control
IE	Control
EE	Control
EL	Control
IE	Control
IL	Control
EE	Control
IE	Control
IL	Control
EE	Control
EL	Control
IE	Control
IL	Control
EE	Control
EL	Control
EL	Control
IE	Control
IL	Control
EE	Control
EL	Control
IE	Control
IE	Control
EE	Control
EL	Control
where the first I/E is thetreatment factor and the second E/L is the
time factor. after preparing a design matrix with the argument
ref="Control" I tried to fit above coefficients.
>From limma userguide chapter 9.3 Common Reference Designs it is
suggested to fit the coefficients on RGList object:
fit <- lmFit(RG, design)
when I tried this I got an error message
Error in array(x, c(length(x), 1), if (!is.null(names(x)))
list(names(x),  : 
        dim<- : dims [product 362880] do not match the length of object
[8]
It seems to me that it is more reasonable to fit the coefficients on
normalized dat and indeed when I trried to fit it on MAList object all
went well.
Is it it a mistake to fit the coefficient on MAList object?
Ron