 
Dear listers,
I am new to the analysis of 2-dye arrays, so please bear with me! 
I have a conceptual question on MA plots and dye swaps.
 
Assume you have 2 arrays, on which Control and Treatment are measured +
its corresponding dye swap. So:
array   Cy3     Cy5
 1      Con    Treatment
 2   Treatment  Con 
 
After normalizing these 2 arrays (e.g. with VSN from within Limma) I
plot the 2 MA plots (based on the normalized data). I would expect that
(in theory) MA plot1 would be the mirrored version of MA plot2. In other
words, normalization per se does NOT take into account dye swaps; this
is only subsequently done in the design matrix when using e.g. limma.
Q: Is this correct? I am asking because in my normalized dataset with
dye swaps (15 arrays total) I do NOT seem to see these mirrored MA plots
when comparing the respective dye-swapped arrays.
 
Thanks,
Guido   
 
Code:
library("limma")
targets <- readTargets("targets_corrected.txt", row.names="Name")
RG <- read.maimages(targets$FileName, source="agilent")
MA.vsn <- normalizeBetweenArrays(RG, method="vsn")
plotMA3by2(MA.vsn)
 
 

------------------------------------------------ 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
email:      guido.hooiveld@wur.nl 



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