[BioC] Analyzing single-channel genepix data from Genepix in Limma

[Lance E. Palmer]

Hi I just wanted some advice on analyzing single channel data from
Genepix in Limma.

There are a number of slides that have bad cy5 signals and other chips
where on cy3 was used, so I wanted to be able to just analyze the cy3
channel.  

After a search of the newsgroup, there was a post by Gordon that
basically says use this:

y2 <- normalizeBetweenArrays(RG$G, method="quantile")
(or use vsn)
and then run Limma normally.

I was wondering if this is still the preferred method?  If one just
passes the cy3 channel values to lmFit, the weights don't seem to be
passed along.  Is there  any way of combining the annotation, weights
and expression values into an object that lmFit can recognize?