[BioC] 2 color Nimblegen data and limma

Carvalho, Benilton bcarvalh at jhsph.edu
Mon Jul 13 23:56:25 CEST 2009

Get the NDF and XYS files from those who generated the pair files.
Then use pdInfoBuilder as described in the vignette to create an
annotation package. Later, you use the oligo pkg to read in the data
and limma as you want. b

On 13/07/2009, at 18:45, "Thomas Hampton" <Thomas.H.Hampton at dartmouth.edu
 > wrote:

> From what I can tell, the way to process Nimblegen data is use
> limma.  The latter does not read Nimblegen ".pair" files, so
> you sort of glue together your own limma-friendly data structures
> and then let limma take over.
> Is that about it?
> Thanks,
> Tom
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