[BioC] Suggestions for Chip-seq differential expression analysis

[Mark Robinson]

Hi Vishal.

I often do differential comparisons of ChIP-seq (or similar) data between experimental conditions using edgeR.  Basically, its 1 step, as opposed to the 2-stage analysis you suggest below.

Basically, you compute read counts for regions of interest across your samples -- for you, this would be a count table of N ROIs by 6 samples.  Then, make your comparison of interest.

Hope that helps.

Cheers,
Mark

On 2010-11-11, at 2:16 AM, Vishal Thapar wrote:

> Hi,
> 
> I wanted some suggestions for a Chip-Seq analysis that I am working on. I
> have ChIP-Seq data for 3 cell types, control, treatment1, treatment2. I have
> 2 replicates of each. I would like suggestions on how I could compare the 2
> treatments to *each* other.
> One way to do this is to do a diff expression for S1= treatment1 vs control
> and S2=treatment2 vs control and then take the regions that occur in S1 and
> S2, get the read counts and do a Chi Square test for each region. Another
> way is to take S1 and S2 regions, get their read counts and use EdgeR from
> there on to do a second differential expression analysis. I am not sure
> which one is better. Any suggestions with justifications are welcome!
> 
> Thanks,
> 
> Sincerely,
> 
> Vishal
> 
> -- 
> *Vishal Thapar, Ph.D.*
> *Scientific informatics Analyst
> Cold Spring Harbor Lab
> Quick Bldg, Lowe Lab
> 1 Bungtown Road
> Cold Spring Harbor, NY - 11724*
> 
> 	[[alternative HTML version deleted]]
> 
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------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: mrobinson at wehi.edu.au
e: m.robinson at garvan.org.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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