[BioC] Normalisation of focussed arrays and Taq-man gene cards

[Aedin]

Dear BioC
What is currently considered the best method of normalisation where the
assumption that most genes are unchanged is invalid?  Is it best to apply
the Li & Wong algorithm or are there other methods that I should consider?

I wish to normalise and analyse the following:
1. A focussed oligonucleotide array. Although this included a good number
invariant "control" genes, most of the genes on the arrays are expected to
change.
2. Arrays in which methylating agents are studied, again a large number
genes on the array are expected to change.
3. Taqman RT-PCR cards.

I would be grateful if you could tell me if I need to consider different
methods for:
A.  oligonucleotide single channel focused arrays,
B.  dual channel spotted focussed arrays

Thanks a million for your advice in this. I appreciate your help.
Best wishes
Aedin