[BioC] how to do quantile normalization under dye swape situation

[yanju]

Hello All,

my microarray datasets are like follows. And I want to normalize the data.
Targets:
Sample    FileName    Dye    Stage    Cy3    Cy5
ZWS57    57.gpr    T5C3    high oblong    ref       high
ZWS58    58.gpr    T3C5    high oblong    high    ref
ZWS61    61.gpr    T5C3    high oblong    ref       high
ZWS62    62.gpr    T3C5    high oblong    high    ref

ref is the commen reference. First I think Within Array Normalization is 
not neccesary (am i right?). Then I want to do the Between Array 
Normalization using "quantile" method to insure the commen reference 
have the same distribution. But with dye swap, I can not use neither 
"Rquantile" nor "Gquantile". What should I do? Or other normalization 
suggestions?

Regards,
Yanju Zhang