Dear all,

My name is Artur Veloso and I am a masters student at the College of
Charleston, South Carolina.
I am using lmFit to analyze arrays that have ndups = 2 and spacing = 1. I
have done all analyses that I wanted with linear models using limma and they
all worked very well. Now I am trying to use the same data on a neural
network to see if I can confirm my results. To do so, however, I need to
extract from Bioconductor a file with the VSN transformed expression levels
for each probe pair. I have the data where all spots were VSN transformed
but the duplicate spots are treated as a unique object only after I apply
lmFit.

I have looked at the user manual, the help page and the function itself and
haven't been able to understand yet. My question is, how should I transform
the replicated spots VSN transformed expression values (using the consensus
correlation from all spots) into just one for each replicate pair at each
array?

Thank you all very much and sorry for what is probably a very simple
mathematical question.

Artur

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