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@kdkorthauer
kdkorthauer committed Feb 27, 2024
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72 changes: 36 additions & 36 deletions lect12-gsea/lect12-gsea.html
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<!DOCTYPE html>
<html lang="en"><head>
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<meta name="generator" content="quarto-1.3.450">

<meta name="author" content="Keegan Korthauer (with slides contributions from Yongjin Park and Paul Pavlidis)">
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<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
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<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
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code span.vs { color: #20794d; } /* VerbatimString */
code span.wa { color: #5e5e5e; font-style: italic; } /* Warning */
</style>
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<style type="text/css">

.callout {
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<p><span class="math inline">\(m=9\)</span>, <span class="math inline">\(n=15\)</span>, &amp; <span class="math inline">\(k=8\)</span>:</p>
<div class="cell">
<div class="cell-output-display">
<p><img data-src="geneset_analysis_files/figure-revealjs/unnamed-chunk-5-1.png" width="480"></p>
<p><img data-src="lect12-gsea_files/figure-revealjs/unnamed-chunk-5-1.png" width="480"></p>
</div>
</div>
</div>
Expand All @@ -859,7 +859,7 @@ <h2>How significant is <span class="math inline">\(q\)</span> overlap in our dis
<p>If <span class="math inline">\(q=3\)</span>:</p>
<div class="cell">
<div class="cell-output-display">
<p><img data-src="geneset_analysis_files/figure-revealjs/unnamed-chunk-6-1.png" width="480"></p>
<p><img data-src="lect12-gsea_files/figure-revealjs/unnamed-chunk-6-1.png" width="480"></p>
</div>
</div>
</div>
Expand All @@ -869,7 +869,7 @@ <h2>How significant is <span class="math inline">\(q\)</span> overlap in our dis
<p>If <span class="math inline">\(q=6\)</span>:</p>
<div class="cell">
<div class="cell-output-display">
<p><img data-src="geneset_analysis_files/figure-revealjs/unnamed-chunk-7-1.png" width="480"></p>
<p><img data-src="lect12-gsea_files/figure-revealjs/unnamed-chunk-7-1.png" width="480"></p>
</div>
</div>
</div>
Expand Down Expand Up @@ -1068,7 +1068,7 @@ <h2>Let’s simulate some gene set data (Efron &amp; Tibshirani 2007)</h2>
<section id="wed-like-a-representative-score-for-genes-within-each-set" class="slide level2">
<h2>We’d like a representative score for genes within each set</h2>

<img data-src="geneset_analysis_files/figure-revealjs/unnamed-chunk-10-1.png" width="960" class="r-stretch"></section>
<img data-src="lect12-gsea_files/figure-revealjs/unnamed-chunk-10-1.png" width="960" class="r-stretch"></section>
<section id="what-will-be-a-proper-gene-set-score" class="slide level2">
<h2>What will be a proper gene set score?</h2>
<p>Can we simply aggregate gene-level z-scores (or t-statistics) within each set?</p>
Expand Down Expand Up @@ -1107,12 +1107,12 @@ <h2>Aggregating z-scores within a set</h2>
</div><div class="column" style="width:.45;">
<div class="cell">
<div class="cell-output-display">
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</div>
</div>
</div>
Expand All @@ -1129,7 +1129,7 @@ <h2>Constructing the null distribution by gene permutation</h2>
</div>
<div class="cell">
<div class="cell-output-display">
<p><img data-src="geneset_analysis_files/figure-revealjs/unnamed-chunk-18-1.png" width="960"></p>
<p><img data-src="lect12-gsea_files/figure-revealjs/unnamed-chunk-18-1.png" width="960"></p>
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</div>
</div><div class="column" style="width:.35;">
Expand All @@ -1152,7 +1152,7 @@ <h2>Constructing the null distribution by sample permutation</h2>
</div>
<div class="cell">
<div class="cell-output-display">
<p><img data-src="geneset_analysis_files/figure-revealjs/unnamed-chunk-20-1.png" width="960"></p>
<p><img data-src="lect12-gsea_files/figure-revealjs/unnamed-chunk-20-1.png" width="960"></p>
</div>
</div>
</div><div class="column" style="width:.35;">
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</div>

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