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GSEA by broad institute is really a powerful tool to handle this analysis very efficiently compared to other packages such as clusterProfiler. Specially it comes with the MsigDB curated genesets for 3 different model organisms. However, there is no curated KEGG geneset available for mmu. I often try to prepare .gmt files using curated KEGG genesets from other tools/repositories. Then GSEA fails to enrichment most of the pathways from the manually curated KEGG genesets. At the opposite when I try to perform the GSEA with other packages "clusterProfiler" then we need to pre-rank the transcriptome dataset manually. Here I struggle performing the Signal2noise ratio calculation and rank them exactly the same as GSEA tool. Therefore, the enrichment plots doesn't show the gene distribution for the genesets as well as GSEA tool. How can I handle this issue more efficiently ?

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    $\begingroup$ There are a lot of questions and issues in this; StackExchange works best when each question is on it's own post. Do you have a specific task that you're trying to do, where GSEA isn't working properly? Any examples you can give about the output you're expecting vs the bad output you're observing would be great. $\endgroup$ Commented Mar 27 at 0:20

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