Question

Method to find pathways different between 2 groups

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Chris ▴ 20

@3fdb6f97

Last seen 4 months ago

United States

Hi all,

I have two groups would like to compare which pathways different between them. I ran gene set variation analysis follow up with limma, fgsea, camera. enrichGO() also rank the pathway but we can't choose which gene set we want to analyze. Each of them gives different result. Haven't tried Qiugen IPA yet. Could we combine the result from each tool? Would you please suggest a method in this case? As Gordon comment on this post Why does GSEA on edgeR results for randomized samples give highly significant p-values?, seem p valule from fgsea is not truly significant as it is. When I search camera limma on pubmed, I found 2 papers. Thank you so much!

fgsea GSVA CAMERA • 1.1k views

ADD COMMENT • link 7 months ago Chris ▴ 20

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Gordon Smyth 52k

@gordon-smyth

Last seen 3 hours ago

WEHI, Melbourne, Australia

When I search camera limma on pubmed, I found 2 papers

I am unclear what point you are trying to make. limma's camera method has been formally cited in nearly 800 published papers.

ADD COMMENT • link 7 months ago Gordon Smyth 52k

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Sorry for not clear! Glad to know camera() is widely used. I just try to find papers use this method for learning purpose. Which gives more context and detail examples, so I may know when to use this method. This paper compare some pathway analysis methods include camera: https://pubmed.ncbi.nlm.nih.gov/29881462/ The conclusion is sigPathway and GSEA are the most powerful methods. There is a post about similar question years ago which I think still haven't had a clear answer. Statistic for GSA

ADD REPLY • link 7 months ago Chris ▴ 20

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sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 2012 paper on camera.

ADD REPLY • link 7 months ago Gordon Smyth 52k

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Thanks Gordon! Don't know why follow by email doesn't work which automatically switch to follow by message.

ADD REPLY • link 7 months ago Chris ▴ 20

score 2 · Accepted Answer · 2024-05-06

Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package EGSEA, described in depth in the publication by Alhamdoosh et al. (2017), which includes camera and GSVA, among others, as optional tools to include in the analysis. If you have questions about the EGSEA package, please remember to add the tag EGSEA to the question.