
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.
 
> Subject: Re: [BioC] chip-chip data
> From: noahd@ucla.edu
> Date: Thu, 4 Mar 2010 19:55:21 -0800
> CC: bioconductor@stat.math.ethz.ch
> To: genome1976@hotmail.com
> 
> Hello Som,
> 
> The Ringo package works quite nicely with Nimblegen arrays. I also used the wonderful Starr package for chip-chip on tiling Affymetrix arrays. After using those packages for looking at data quality and normalization there are some graphical tools and analysis tools (like finding the chip-enriched regions) too, but many other packages can work with the data in the resulting Ringo/Starr derived expression sets.
> 
> noah
> 
> 
> On Mar 4, 2010, at 4:27 PM, somnath bandyopadhyay wrote:
> 
> > 
> > Hi there,
> > 
> > I am trying to analyze chip-chip data from Nimblegen 385k arrays for histone methylated regions. I have replicates from both wild type and knock out cells with separate inputs (controls) for the KO and WT. That makes a total of 12 arrays. I was wondering if anybody could help me in pointing at the right package or tools. I am new to chip-chip data.
> > 
> > 
> > 
> > Thanks in advance,
> > 
> > Som.
> > 
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