[BioC] vsn in limma or marray/arrayMagic

[A.E.Schiel at lumc.nl]

Dear all,
I do have a probably simple question, is running "vsn" in limma (normalizeBetweenArrays) the same as running "vsn" in marray or arrayMagic?
My Boxplots suggest that there is a difference and I was wondering if someone can give me a hint why that might be. 
My particular problem is that I would like to use the fact that my probes are spotted in duplicates but not the spacing limma expects. I therefore want to first normalize all my arrays (22), then export the data to a text file and resort that file to get the right spacing. If I am right I should be able to read such a text file with read.maimages into limma and then continue with my analysis. Therefore I would like to know if I need to do my normalization with marray (or arrayMagic) or if I can use vsn in limma?
Many thanks in advance,
Anja


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