Visualise gene set analysis plot
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@jaynishshah-17569
Last seen 3.0 years ago

Hi there,

I used DESeq to identify differentially expressed RNAs in my two samples. I have moderated t-test statistics that I used in limma's cameraPR() function and got GSA scores with p-values.

How do I plot this data similar to the enrichment plot that Broad Institute's GSEA Java app produces? Here's how it looks. https://www.google.com/search?q=GSEA+broad&source=lnms&tbm=isch&sa=X&ved=0ahUKEwirk4Kh9NzdAhWK6YMKHQodAiEQ_AUIDygC&biw=960&bih=534#imgrc=nZFTQ2YoFMG9OM:

Thanks

Jay

gene set analysis gene set enrichment limma • 496 views
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@gordon-smyth
Last seen 9 hours ago
WEHI, Melbourne, Australia

See the barcodeplot() function. Examples of its use can be seen in the following workflows:

https://www.bioconductor.org/packages/devel/workflows/vignettes/RnaSeqGeneEdgeRQL/inst/doc/edgeRQL.html

https://f1000research.com/articles/5-1408

https://f1000research.com/articles/6-2055

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