Question: GSEA after MACS2 peak calling for ChIP-seq; want positive enrichment only
gravatar for dariasc
4 days ago by
dariasc0 wrote:

Hello, I have called histone modification ChIP-seq peaks compared to a control using MACS2 and annotated them using Homer.

I then try to perform pre-ranked GSEA. I only have positive values in my ranking, but I also get negative enrichment so I think GSEA is treating the genes at the bottom of my list as negatively enriched. But they are not; they are just lower but positive. Is there a solution for this? I tried choosing the 'classic' option rather than 'weighted' and it doesn't do it.

Also, what would be the best scoring for pre-ranking? I have fold enrichment, peak score, q-value, p-value and pileup value for each gene.

gsea chip-seq macs2 • 50 views
ADD COMMENTlink modified 4 days ago by alserg340 • written 4 days ago by dariasc0
gravatar for alserg
4 days ago by
alserg340 wrote:

Development version of fgsea (from github) supports one-tailed tests. However, we don't see much of a difference compared to a standard approach. See here in more details:

ADD COMMENTlink written 4 days ago by alserg340
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