[BioC] 2 color Nimblegen data and limma

Thomas Hampton Thomas.H.Hampton at dartmouth.edu
Tue Jul 14 04:18:24 CEST 2009


Thanks very much.

Which normalization do you suggest, given that I retrieve the
NDF and XYS files?


Am I on the right page, and, do you think
On Jul 13, 2009, at 5:56 PM, Carvalho, Benilton wrote:

> 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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