GSEA Tool to use with RNA-seq data

Question

[restonpiston]

Hello, I'm working with a set of RNA-seq data which I want to analyze the Gene Ontolgy Enrichment and the metabolic pathways from Kegg. I have already checked the Pathways and the GO using the hypergeometric test, but I wanted to cross check the results using the Gene Set Enrichment.

Optimally I would like a tool that takes the output of Deseq in some shape and form and runs the GSE test. I have tried GSEA but the results are not what I was expecting (using the metric of -log(pvalue) * sign(logFC)). What tools are currently being used successfully for this kind of analysis?

[russhh]

I use the same score in my ranking function. For GSEA and enrichment, I use clusterProfiler: http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html

You can pass in pathway annotations from msigdbr, reactome, GO, KEGG etc etc

[restonpiston]

Thanks for the answer! I have managed to use it and it works pretty well, even tho I had to modify my data a bit, as I am using custom pathway annotations.

Answer 1

[Buffo]

To date, WebGestalt is probable the best tool for GSEA analysis. You can use any ranked list, such as the log2fold from deseq.

[restonpiston]

Thanks for the answer! Unfortunately, I do not seem to be able to have it working. I have input the data like this:

Maybe you could tell me what I am doing wrong? I am receiving "R error (1565083554)".

[Buffo]

Yes, I have noticed that error, FDR as a significance level apparently is not working, change it to TOP 30 (for example). This page is in continuous and exhaustive updates, so I hope it will be fixed soon.