Dear Bioconductor users,
 
I am trying to analyse expression experiment carried in two different Affymetrix facilities. The arrays from the two facilities show a significant difference in expression medians, and this difference persists when I use normalization such as RMA (with all the arrays togather). I would like to scale the CEL files and save the scaled data in the same format so I can use the new objects with the probe-level normalization methods offered by bioconductor, normalizing all the arrays together (i.e not just simple data frame of the expression values, but an object accepted by exspresso() or other functions). 
 
 
Any help will be greatly appreciated,
 
Thanks, Garry


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