[BioC] Limma vs Maanova, and use of covariates

[Ingunn Berget]

Hi

I believe there are two approaches for using ANOVA with microarrays,

1) Calculate logratios, do normalisation and then fit the experimental 
conditions by an ANOVA model, or
2) Use the intensities of each channel, transformed with appropriate 
transformation (log, linlog.logshift,...), and use array, dye, spot effect 
and so in the ANOVA model in addition to the experimental conditions. Which 
means that the normalisation is done by factors in the ANOVA model

limma is much used for the first approach, whereas I think Maanova is more 
used for the second approach.

Does anybody have any experience on both approaches? WHat is recommended?
Can the limma package be used for the second approach?

Additional question: Can continuous covariates be fitted with limma?
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Ingunn Berget
Norwegian University of Life Sciences
Department of Animal and Aquacultural Sciences
Boks 5003
1432 Ås
Norway