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'

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' > >

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 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK