[BioC] Save rma normalization results for later use

[Christian Ruckert]

I have a bunch of 2000 arrays I want to normalize with rma() from affy 
package. Then from time to time there will be single arrays to be 
analyzed together with these 2000. To apply the same normalization 
procedure to the single arrays later I want to split the rma step in its 
elements.

bg.correct(data, method="rma")
As it's array wise I think no problem for the single array.

normalize(data,  method="quantiles")
I think here I need to save the mean values for each row to normalize 
the single array later with this values (I know it's not totally exact 
but I think acceptable). In my understanding of the quantile 
normalization the sorted perfect match values should be exactly the same 
for every sample, but I got differences.

So my questions are:
1. How does the last step look to got exactly the same results as with rma()
2. Why the differences in quantile normalization?
3. Is there a better way to handle this task?

Any help would be appreciated,

Christian