I want to perform GSEA analysis with
clusterProfiler package and I am following this post . But I have few doubts (and be patient, I am a biologist):
- Is it better to perform GSEA using the Ensembl ID or the gene symbol?
I did it with both Ensembl & gene names just to see if I was getting the same results but surprisingly I got slightly different results. I am not sure which one should I choose since I don't want to be biased based on what would fit/support better my hypothesis (which is the one run on the gene symbol).
- in the first figure (dotoplot) of the website I posted, the enriched terms are divided by activated and suppressed which reflect whether the enrichment score (ES) is positive or negative. A positive ES indicates gene set enrichment at the top of the ranked list whereas a negative ES indicates gene set enrichment at the bottom of the ranked list. but what does it mean practically? What does it tell me that e.g. cytosol ribosome (in the figure) has negative ES so it is at the bottom of the ranked list?
thank you in advanced