Hi Mark,

Thanks for your reply. I have used EdgeR for a paired comparison without a
control but I haven't used it with one. Would you point me to a simple
tutorial or just even the function in EdgeR that can help me do that? The
way I understood edgeR was, that its for a paired comparison with
replicates. Here, I have 3 comparison. I did look at one tutorial online but
it doesn't mention anything about a 3 comparison with 1 being a control. May
be I am missing something here.

Thanks again for your help.

Sincerely,

Vishal

On Wed, Nov 10, 2010 at 5:41 PM, Mark Robinson <mrobinson@wehi.edu.au>wrote:

> 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@wehi.edu.au
> e: m.robinson@garvan.org.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
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