GSEA enrichment analysis

Question

[mysskks]

I tried to GSEA enrichment analysis. To do this, I try to make two groups such low and high expression groups. I try to find other articles what is cutoff percent. Cutoff percentage are diverse among articles.

Can i make two groups by myself ( such as low(50%), High(50%) or low(40%), high(40%))???

Thank you for reading this

[h.mon]

I don't understand your question, but is it related to 'Question: Cut-off for genesets in GSEA?

Or are you talking about a cutoff for defining your candidate set for an over-representation analysis? If that is the case, this is not a GSEA, as GSEA is a cutoff-free analysis to test for enrichment. Read the introduction of this or this papers for clarification.

[mysskks]

Thanks for kind answers. I did kaplan meier survival analysis by using RNAseq data in TCGA. And I found cut off value of survival by using cutoff finder. Is it ok make up and low groups by using cut off value of survival??

Answer 1

[BioinfGuru]

You can make what ever groups you like. However, I suggest your cuttoff should be a fold change, p-value, or even better a q-pvalue

[mysskks]

Thanks for kind answers. I did kaplan meier survival analysis by using RNAseq data in TCGA. And I found cut off value of survival by using cutoff finder. Is it ok make up and low groups by using cut off value of survival??