[BioC] Normalization of arrays where most of the genes change

[He, Yiwen (NIH/CIT) [C]]

Hi,

We have some arrays where most of the genes are turned on under certain conditions. This violates the assumption that most normalization methods make. What would be the best way to handle such arrays? We are using Agilent arrays but as I understand the platform should not matter. I'm wondering, if LOESS or Quntile normalization can be used on a (small) subset of invariable genes and expand to the whole array? If so, is there such a tool in BioC?

Thank you very much!

Yiwen He
DCB/CIT/NIH