[BioC] chip-chip data
Joern.Toedling at curie.fr
Sat Mar 6 09:58:21 CET 2010
there also is a Plos Computional Biology article, which also provides many
details on how to use Ringo:
You may also want to have a look at the associated data package "ccTutorial".
On Fri, 5 Mar 2010 11:42:30 -0800, Noah Dowell wrote
> The vignettes for Starr and Ringo are quite helpful for getting
> started on reading in your files, processing and normalization.
> There is also a publication associated with Ringo for a little more
> explanation. It seems like you have all of the files so just fire
> up Ringo and see how it works :). (There are example data "made" for
> Ringo that you can use to test it out and make sure your files look
> like they "should.")
> Here is the link to the vignette:
> And the paper citation:
> J. Toedling, O. Sklyar, T. Krueger, J. J. Fischer, S. Sperling, and
> W. Huber. Ringo - an R/Bioconductor package for analyzing ChIP-chip
> readouts. BMC Bioinformatics, 8:221, 2007.
> I am certainly not the expert on this board but if you start to get
> specific errors (on your data analysis) after you read through the
> vignette and worked with the example data then post them and I will
> do my best to help out.
> Hello Noah,
> Thanks for the suggestions. Do you have a protocol or something for
> Starr or Ringo? I am starting from .pair, .ndf, .pos and .gff (for
> the nimblegen refseq mouse genome) nimblegen files. I would really
> appreciate it if you would share your protocol/s.
> Thanks so much,
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