[BioC] Nimblegen data: oligo, affy, limma?

[J.delasHeras at ed.ac.uk]

I have been using limma for a little while, for the analysis of 
2-colour cDNA arrays.

I am going to get pretty soon some data from Nimblegen. This will be on 
their promoter arrays, hybridised with some ChIP samples. I understand 
it follows a similar format to Affymetrix, but they use 2-colour hybs.

I'm wondering as to the best way to analyse these. I checked the BioC 
archive for "nimblegen" and I got a couple of things to consider, but I 
am still not sure.

Initially I thought that 'affy' would be the way to go, but since it's 
a 2-colour hyb, I suppose that 'limma' could handle it. In fact, from 
limma I could choose to treat the data as single channel arrays if I 
had to, and I am already familiar with limma. The things I have to 
consider is what method to normalise the data. I read that Loess might 
not be such a good idea for this type of data (ChIP on promoter 
arrays), and perhaps Aquantile would be best. I don't know. I'll have 
to check further. Any pointers greatly appreciated.

Then I found that there's a package somewhere (didn't see it in BioC) 
called 'oligo' that seems to support Nimblegen data, so I would like to 
look into that too. Again, any comments as to how useful this is, 
especially in comparison with limma, would be great.

thanks for your help!

Jose

-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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