[BioC] Nimblegen analysis using Bioconductor

[Joern Toedling]

Hi Rene,

you are right, you can use oligo and makePlatformDesign. I had faced the
same problem with my NimbleGen expression data and, of course, the
optimal solution is to call NimbleGen's technical support. However, in
the meantime, the information of the xys files was basically contained
in the ftr (feature report files) that I only had in the beginning. My
package Ringo contains a simple function "ftr2xys" which does the
conversion of ftr files into xys files.
Hope this helps. Please let me know, if you encounter problems with the
function.

Regards,
Joern


Rene Dreos (JIC) wrote:
> 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'
>
>