[BioC] normalisation for universal reference in 2 channel arrays

[Peter Wilkinson]

I would like to know some alternative to normalization for 2 channel 
experiments against universal, where samples may have been hybridized in 
seperate batches where the universal RNA has changed lot (should not have 
happened but it did). What is the same between the batches is that what 
looks like up-regulated compared to the universal iis upr-egulated, and 
what is down-regulated looks down-regulated. The difference is that the 
down-regulated (and not in the up), so so much more down-regulated in one 
of the batches. It looks like to be that the universal has more mRNA 
abundance in one batch over the other.

so ...

I have samples that can be divided into 2 classes: 0,1, and within each 
class I have samples that have been run at different times. I would like to 
treat my universal channel uniformly across all samples (assuming that my 
universal changed lot), and then adjust the Sample (Red) channel to that.

is the normalizeBetweenArrays with the method="Gquantile" option the right 
option for this?

What is the complete work-flow for this case? And after I have normalized 
within the Arrays, can I go on to scale option for normalizing between arrays.

Peter