<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>

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2021-07-13T13:09:00.567Z
2021-07-13T13:09:00.567Z
An Ignorant Wanderer
<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>

<gsea>
GSEA: Computing an Enrichment Score (as described in the original paper)
# 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

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## 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


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