[BioC] Building an annotation data package - not Affymetrix

[Lavinia Gordon]

   Hi Sean
   Many thanks for your email.
   I have tried most of the packages that you mention and have had some very
   pleasing results.
   Specifically I am interested in using the cPlot function of geneplotter.  I
   could not see a similar function in any other packages (genome wide as
   opposed to just chromosome wide display).
   with regards
   Lavinia.
   At 07:46 AM 5/08/2009 -0400, Sean Davis wrote:

     On    Wed,    Aug    5,   2009   at   4:28   AM,   Lavinia   Gordon
     <[1]lavinia.gordon at mcri.edu.au> wrote:

     Â  Dear all
     Â   I  would like to use the package 'geneplotter' which requires a
     Bioconductor
     Â  data package.
     Â   I cannot see a Bioconductor data package for the Nimblegen HG18
     promoter
     Â  arrays, so I will need to make my own.
     Â  Based on what I can see in the mailing list, I believe that I need to
     use
     Â  AnnotationDbi, and modify the function makeProbePackage to read in
     NimbleGen
     Â  (as opposed to Affymetrix data).
       Could  anyone confirm that I am on the right track?/show me any useful
     Â  pointers?
     Â  with many thanks for your time,
     Â

     There  are  other ways to go here.  You could try the Ringo, ACME,
     tilingArray, or oligo packages for data import and analysis.  Each also
     has graphical functions for output.  For graphics, you could additionally
     look at GenomeGraphs and rtracklayer.Â
     Sean
     Â

   Lavinia Gordon
   Research Officer
   Bioinformatics
   Murdoch Childrens Research Institute
   Royal Children's Hospital
   Flemington Road Parkville Victoria 3052 Australia
   telephone: +61 3 8341 6221
   [2]www.mcri.edu.au
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References

   1. mailto:lavinia.gordon at mcri.edu.au
   2. http://www.mcri.edu.au/