[BioC] Limma and Dye-Swap/Single Channel

[S_Thieme]

Hello,

I hybridized for two samples both Cy3-Label and Cy5-Label to one chip (i.e. 
wtCy3+wtCy5 and mutantCy3+mutantCy5.
I would like to normalize that data, but how?
I tried to use the array2channel funtion, but how do I use the result?

My targets looking like this:
   FileName Cy3 Cy5
1 e85b.txt  WT  WT
2 e87b.txt  WT  WT
3 e88b.txt 139 139
4 e89b.txt 139 139

After array2channel:
     Channel FileName Target
1.1       1 e85b.txt     WT
1.2       2 e85b.txt     WT
2.1       1 e87b.txt     WT
2.2       2 e87b.txt     WT
3.1       1 e88b.txt    139
3.2       2 e88b.txt    139
4.1       1 e89b.txt    139
4.2       2 e89b.txt    139

Can I get a model.Matrix out of that? Or is it not possible to normalize 
that way of hybridization?

Thanks!

Sebastian

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