Question: GSEA Tool to use with RNA-seq data
0
gravatar for restonpiston
14 months ago by
restonpiston30
restonpiston30 wrote:

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?

gsea rna-seq • 1.3k views
ADD COMMENTlink modified 14 months ago by Buffo1.8k • written 14 months ago by restonpiston30
1

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

ADD REPLYlink written 14 months ago by russhh5.5k

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.

ADD REPLYlink written 14 months ago by restonpiston30
1
gravatar for Buffo
14 months ago by
Buffo1.8k
Buffo1.8k wrote:

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

ADD COMMENTlink written 14 months ago by Buffo1.8k

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

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

ADD REPLYlink written 14 months ago by restonpiston30

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.

ADD REPLYlink written 14 months ago by Buffo1.8k
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