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

[Sean Davis]

On Friday 01 September 2006 06:47, J.delasHeras at ed.ac.uk wrote:
> 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.

Nimblegen arrays are actually more similar to two-color arrays, in many 
respects (at least for the chip-chip application).  The manufacturing process 
is similar to Affy (light-directed synthesis), but for the chip-chip 
application, you can think of them as two-color arrays.  The file formats for 
nimblegen are also similar to many two-color platforms (tab-delimited text) 
and so can be easily read using read.table() and the like.  As for 
normalization, that will depend on the analysis method that you are using, to 
some extent.  Do you need a "between-array" normalization or not?  Do you 
require that a "center" for each array be specified for the purposes of 
analysis?  Finally, the actual biologic situation may make a difference.  
Pull-downs of things like histone markers tend to produce very strong signals 
while pulldowns of early developmental transcription factors in 
differentiated cells produce few signals that are not strong.  

As for the oligo package, it is available in the development archive 
(bioc-1.9).  

Sean