Hi

I have multiple Affy methylation tiling arrays, (i.e. _me and _in) arrays 
which have been sorted into functional groups, i.e. group 1 (cancer), group 
2 (cancer) and group 3 (normal)

I normally run Illumina arrays for methylation and so I'm not massively 
confident with this platform. I've managed to import my arrays in, and 
analyse them with regionStats.

What I want to do is try a probe level comparison of the three groups, i.e. 
group 1 vs. group 2; group 1 vs. group 3 and group 2 vs. group 3 for 
significance, i.e. I need a coefficent and p-value. 

I would normally use limma to construct a model, but I can't see how limma 
could be applied to the dataset output by regionStats 

Has anyone any experience with his?

BW

Andrew

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