Answers.Body: <p>Actually I believe I get it now. i is not a constant. We vary it from i=1 to N and consider the i for which <span class="math-container">$P_{hit} - P_{miss}$</span>  is largest in magnitude</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-07-13T13:09:00.567Z
Answers.LastActivityDate: 2021-07-13T13:09:00.567Z
Answers.UserDisplayName: An Ignorant Wanderer
Body: <p>The following paragraph comes from the GSEA paper that explains how to obtain an enrichment score for a gene set. Note that the enrichment score is computed <strong>up to a position i</strong> in L. There are 2 things I don’t understand about this:</p>
  <p>1- first, the following image illustrating the method seems to suggest that that we score a gene set across the whole list of ranked genes, which conflicts with the idea of “up to a position i” in L</p>
  <p>2- second, if we’re only considering genes up to a position i, then how are we going to capture the genes that are underexpressed (appear at the bottom of the ranked list) for phenotype A?</p>
  <p><a href="https://i.sstatic.net/guDWR.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/guDWR.jpg" alt="enter image description here" /></a>
  <a href="https://i.sstatic.net/Wh35F.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Wh35F.jpg" alt="enter image description here" /></a></p>
  
Tags: <gsea>
Title: GSEA: Computing an Enrichment Score (as described in the original paper)
ThreadText: # GSEA: Computing an Enrichment Score (as described in the original paper)
  
  (Asked by: username_0 on 2021-07-10)
  
  The following paragraph comes from the GSEA paper that explains how to obtain an enrichment score for a gene set. Note that the enrichment score is computed **up to a position i** in L. There are 2 things I don’t understand about this:
  
  1- first, the following image illustrating the method seems to suggest that that we score a gene set across the whole list of ranked genes, which conflicts with the idea of “up to a position i” in L
  
  2- second, if we’re only considering genes up to a position i, then how are we going to capture the genes that are underexpressed (appear at the bottom of the ranked list) for phenotype A?
  
  [![enter image description here](https://i.sstatic.net/guDWR.jpg)](https://i.sstatic.net/guDWR.jpg)
  [![enter image description here](https://i.sstatic.net/Wh35F.jpg)](https://i.sstatic.net/Wh35F.jpg)
  
  **Tags:** gsea
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2021-07-13. Score: 2 | Accepted answer
  
  Actually I believe I get it now. i is not a constant. We vary it from i=1 to N and consider the i for which $P\_{hit} - P\_{miss}$ is largest in magnitude
  
  
  ---
  
  