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!

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

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.

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