[BioC] loop design with limma

[Ron Ophir]

Dear all,
>From what I understood to when I read-- Kerr, M. K., and G. A.
Churchill 2001 Statistical design and the analysis of gene expression
microarray data. Genet Res 77(2):123-8--, to analyze loop design
correctly one needs to assess the dye effect and the spot effect. In the
model M+AD+(AD)+G+(AG)
(DG)+(VG), the interaction of the arrays and genes(AG) and the
interaction of dyes and genes (DG) should be 0. Thus, analysis based on
this model should use the measurements of each channel separately rather
than using the channels ratio. In limma, after normalizing, we left with
M and A values and if what I described above is correct I don't
understand how to analyze loop design in limma.
Is there a way to get the normalized channels rather than the
normalized ratios?
Thanks,
Ron

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