GSEA analysis

Question

[sarahawan92]

I ran the analysis in GSEA software and got the plots. But the plot doesn't look the way it has to be. I am posting one of the plot. kindly give me feedback where is the problem.

[Ram]

Like I have told you before, please use proper tags. Hi is not a subject-matter tag. It is quite presumptuous of you to ignore advice provided to you, never provide feedback on people contributing to your posts and criticize moderators for asking that you invest more effort.

[cvenkat95]

The problem is in framing the question. Please explain what exactly you are trying to achieve. Only screenshots give no information.

[sarahawan92]

No worries . I can addressed again. I have attached the plot above which i got from my GSEA analysis. In the plot I am unable to see the negative phenotype. Usually we always found postive and negative phenotype in GSEA plot. But in my case I can’t find the negative phenotype. Can you please give me your feedback on the plot which i ahev attached above. I hope now it makes some sense to you. Thanks

[cvenkat95]

I am not sure if this helps, since your question is vague and open-ended. Anyway, after you do your analysis through the GSEA tool, an 'index.html' file is generated with the enriched gene sets for positive and negative phenotypes, along with detailed enrichment results. If you have no enriched gene sets in the negative phenotype, you might have to go back and check the following:

1. If you run Pre-Ranked, then try ranking the genes through a different metric (p-value is not a good ranking metric).
2. Try using different gene sets, narrow or expand them.