The function limma::residuals.MArrayLM ignores the 'design' argument.

The current code is:

fitted.MArrayLM <- function(object,design=object$design,...)
#    Fitted values from MArray linear model fit
#    Gordon Smyth
#    29 November 2005
{
    object$coefficients %*% t(object$design)
}

and should be changed to 

fitted.MArrayLM <- function(object,design=object$design,...)
#    Fitted values from MArray linear model fit
#    Gordon Smyth
#    29 November 2005
{
    object$coefficients %*% t(design)
}

Thanks for bringing this to my attention.

The current code is actually correct. Rather than changing the code, I will remove the 'design' argument, because there are no circumstances in which it would be reasonable to supply an external design matrix.

The reason for the spurious argument is historical. In the very beginning, MArrayLM fitted model objects didn't store the design matrix, but now they do.