I am analyzing an RNA-seq dataset using GSEA, and I have strong enrichment for both the "MEK_UP.V1_UP" and "MEK_UP.V1_DOWN" gene sets. How can this be explained?
Hi Savannah
too much differences between both groups?
is there a technical bias between groups that could enhance differences?
or phenotypes, distanced from each other?
fred
Firstly, you should check the gene set. Are these two "MEK_UP.V1_UP" and "MEK_UP.V1_DOWN" the same or not? Because the GSEA analysis only requires the gene symbols, you should be careful about the gene inputs. Specifically, you should distinguish the UP genes and DOWN genes in some cases. Secondly, when you use the GSEA software, you should also check the expression levels between the two groups. Theoretically, these two gene sets present the opposite ways.
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