Question: Visualise gene set analysis plot
0
gravatar for jaynishshah
13 months ago by
jaynishshah0 wrote:

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

ADD COMMENTlink modified 13 months ago by Gordon Smyth39k • written 13 months ago by jaynishshah0
Answer: Visualise gene set analysis plot
1
gravatar for Gordon Smyth
13 months ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

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

ADD COMMENTlink modified 13 months ago • written 13 months ago by Gordon Smyth39k
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