Hello!
I have trouble understanding the enrichment score of a GSEA.
I am running DESEQ2 on two groups, ex. control vs treatment. Then, using the output to run a gene set enrichment analysis (clusterprofiler - gseGO).
I get enrichment scores between -1 and +1, which means negative and positive enrichment of specific gene sets.
Is it possible to tell where the difference comes from? Whether a positive enrichment means enrichment in the control or treatment group?
Thank you!
You might get more accurate help if you ask at the support site of Bioconductor: https://support.bioconductor.org
You could use fsgea in Bioconductor to plot and calculate the enrichment for each gene set, this might help you to understand where does this come from. But to understand that you'll need to read the original paper.
Positive and negative meaning depend in how you made your comparison but it is positive if the gene set is located more in the positive region of the vector and negative if they are in the negative region. Are you doing Control - treatment or Treatment -group in DESeq2?
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