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how to calculate running sum in R for GSEA

Hello,

I am trying to implement a R function which does the GSEA.

I read many papers related to this method and each of them tries to destroy the other and show a better performance of its own method (that is what we do as scientists :-D )

Anyway, what I am now working on is to find out how running sum works to calculate the Score!

The running sum is to calculate the Enrichment Score over a gene set

  1. How to define a gene set? For example if I have over 20000 genes, can I say the first 200 are one set, and the rest is another set?
  2. How to calculate it ? what they say

a Kolmogorov-Smirnov (K-S) running sum statistic is computed: beginning with the top-ranking gene, the running sum increases when a gene annotated to be a member of gene set S is encountered and decreases otherwise

Can someone explain how does this technique work?

Can it be done for one sample? If not, why?

gsea r microarray
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updated by Ram Ram • written by Mo Mo

1 answer

The GSEA algorithm is already implemented in other R libraries. For example you can check the functions gseGO or gseAnalyzer from the clusterProfiler package. Check also the vignette for more examples.

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updated by Ram Ram • written by Giovanni M Dall'Olio Giovanni M Dall'Olio

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