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

[Gordon Smyth]

Dear Paul,

It may not affect your plot much, but be aware that the model you 
fitted includes a probe-specific dye-effect (the intercept term), so 
that dye-swapping is not exactly equivalent to multiplying by -1 
according to the model. This doesn't change the fact that the fitted 
values should follow the data values in your plot.

Best wishes
Gordon

At 09:44 AM 2/05/2007, Paul Shannon wrote:
>I failed to explain that I multiplied all of the measured dye-swaps
>(cy5/cy3) by -1 so that their ratios would be easy to compare to the
>(cy3/cy5) ratios.
>
>  > 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,]))