[BioC] chip-chip data

[Joern Toedling]

Hi Som,

there also is a Plos Computional Biology article, which also provides many
details on how to use Ringo:
http://tinyurl.com/ydvrjq8
You may also want to have a look at the associated data package "ccTutorial".

Best regards,
Joern

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:
> 
> Ringo:
> 
>
http://www.bioconductor.org/packages/release/bioc/vignettes/Ringo/inst/doc/Ringo.pdf
> 
> 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.
> 
> noah
> 
> 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,
> Som.
> 

---
Joern Toedling
Institut Curie -- U900
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246927