Seby, If you actually want the normalised R and G intensity values rather than the MA values there is a simple function in limma to convert your normalised MA list to a RG list. >RGnorm <- RG.MA(MA) >write.table(RGnorm$R, file="Rvalues.txt") >write.table(RGnorm$G, file="Gvalues.txt") Regards, Matt