[BioC] Nimblegen analysis using Bioconductor

[J.delasHeras at ed.ac.uk]

Quoting "Rene Dreos (JIC)" <Rene.Dreos at bbsrc.ac.uk>:

> Dear list,
> I am a Bioconductor user and I would like to use its to analyse
> Nimblegen expression chip for tomato, both 60 mer and 24 mer platforms
> (unfortunately I don't know the ID for the 60 mer, for the 24 mer is
> 968).
> I know that usefull packages for this type of analysis are the oligo and
> makePlatformDesign. Unfortunately they need a particular file (.xys)
> that I haven't. I read in bioconductor mailing list that the easier way
> to have them is to contact the technical support @ Nimblegen. I try to
> contact them but nothing happened... Could someone provide them for me?
> Kind regards
> Rene'

You can get them from tech support, but I agree, sometimes they're not  
the fastest to reply. I get the feeling that they're a little  
under-staffed in that department.
I believe you can also use Ringo, without the XYS files.
I don't use XYS files either, I just make manually an RGList object  
from the raw data, and use the package Limma for my analyses...

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
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