[BioC] limma question: direct two-color design & modeling individual subject effects

[Gordon Smyth]

At 09:44 AM 2/05/2007, Paul Shannon wrote:
>  > How have you obtained "fitted values"?
>
>I multiplied the model by the fitted coefficients, summed the 
>resultant vector,
>and corrected for dye swap:
>
>     # corrector = 1 or -1
>     corrector * sum (model [slide,] * efit$coef [row,]))

Note that in limma

    fv <- fitted(fit)

also works. It gives a matrix of fitted values.

Best wishes
Gordon