Ranking the GSEA Results
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@4aa9b7a6
Last seen 4 months ago
India

I have a query regarding the analysis of GSEA Results. For GSEA, I have used "fgsea" R package to obtain the dysregulated KEGG pathways. Now, I want to rank the dysregulated KEGG pathways.

I have seen people ranking the dysregulated genes on the basis of log2Fold Change and p-value obtained from DESeq2. For genes, they use the decreasing order of log2FC * (-log10 p-value) to rank the genes.

So, is it logical to use NES * (- log10 Nominal p-value) for ranking the KEGG pathways?

Edit: The idea was inspired by people ranking the DEGs for preranked GSEA using their log2FC * (-log10 p-value). Also, the GSEA results I am getting, don't have any pathway with adjusted p-value <0.25. So, I can't rank the results by absolute NES after taking cutoff by p-adjusted value.
fgsea log2FC • 1.1k views
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Where did you see ranking of genes by log2FC * (-log10 p-value)? I don't think I ever saw one and not sure what it should achieve. Aren't you confusing it with ranking by sign(log2FC) * (-log10 p-value)?

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I found the suggestion of using log2FC * (-log10 p-value) here.

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You can rank the output of GSEA by the NES there is no need to use the p-value for ranking. Why do you think it is needed?

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The idea was inspired by people ranking the DEGs for preranked GSEA using their log2FC * (-log10 p-value). Also, the GSEA results I am getting, don't have any pathway with adjusted p-value <0.25. So, I can't rank the results by absolute NES after taking cutoff by p-adjusted value.

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You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so using log10(p-value) won't solve your problem.

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There GSEA has been run on 3 sets of samples. For 2 of them, GSEA results in statistically significant KEGG pathways with adjusted p-value <0.25 while not for the 3rd set.

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Then you meant to ask a different question? Each time we try to help we are getting answers that points us to a different direction. We cannot help you this way without spending quite a lot of time. Please provide the minimal necessary context and code to help you. Good luck!

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@mikelove
Last seen 4 days ago
United States

Some posts on this topic:

https://www.google.com/search?q=site%3Asupport.bioconductor.org+GSEA+ranking+DESeq2
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Thanks for replying. On searching on the web, I am finding the results answering how to rank the genes for using GSEA. However, I want to rank the GSEA results.

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Sorry I missed that when replying.

GSEA is not a Bioconductor package right? So the developers aren't here to provide their recommendation. This support site is generally reserved for Bioconductor package help.

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I have actually used the "fgsea" Bioconductor package which is used for GSEA. Thanks for pointing that out. I have edited that in the original post.

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Got it. So then I'll take off DESeq2 as its mostly a downstream question. You may need to direct the fgsea developer to the thread. When you post originally it sends an email to the developer (hence I came here) but i don't think it does this when you change tags.

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Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself

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