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Old 05-20-2014, 04:30 AM   #5
Location: Middle East

Join Date: Apr 2013
Posts: 74

Many thanks @dpryan for the prompt reply.
I am sorry if I missed some information. I just wanted to make my question simple. What I want exactly to do is:
to find the expression profile (vector of 20 values for 20 cell types) at each genomic region (e.g. promoter) and compare it with the epigenomic profile (vector of 20 values of histone modification marker or methylation..etc for 20 cell types) in order to detect those regions that have strong correlation.

So, your point is to keep the replicates. In this case, I will need to use the same epigenomic value (histone modification value or methylation..etc) with the n replicates of the same cell type.

I am not sure if GSEA Can do this task for me?
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