how to perform pre ranked GSEA in R?
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Nemo ▴ 80
@nemo-7332
Last seen 3.6 years ago
India

I have a list of probes (up regulated genes) and I have a gene set (consists of several column of probes which have been already ranked based on their expression) 

Now, I want to perform  Kolmogorov-smirnov test or pre ranked GSEA. can any body help with how to do it ? you can find an example data in the following links

 

r microarray statistics GSEA • 1.3k views
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@samuel-collombet-6574
Last seen 4.3 years ago
France

Hi Nemo,

You can use the topGO package, the vignette shows example on how to do it :)

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predeus • 0
@predeus-9207
Last seen 17 months ago
United States

use fgsea bioconductor package.

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