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]]

