[BioC] chip-chip data

[Noah Dowell]

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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