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welcome.html
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<!DOCTYPE html>
<html lang="en"><head>
<script src="welcome_files/libs/clipboard/clipboard.min.js"></script>
<script src="welcome_files/libs/quarto-html/tabby.min.js"></script>
<script src="welcome_files/libs/quarto-html/popper.min.js"></script>
<script src="welcome_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="welcome_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="welcome_files/libs/quarto-html/light-border.css" rel="stylesheet">
<link href="welcome_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="welcome_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles"><meta charset="utf-8">
<meta name="generator" content="quarto-1.3.450">
<meta name="author" content="22th - 26th April 2024">
<title>Introduction to Biostatistics and Machine Learning</title>
<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">
<link rel="stylesheet" href="welcome_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="welcome_files/libs/revealjs/dist/reveal.css">
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
vertical-align: middle;
}
</style>
<link rel="stylesheet" href="welcome_files/libs/revealjs/dist/theme/quarto.css">
<link href="welcome_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
<link href="welcome_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
<link href="welcome_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
<link href="welcome_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
<style type="text/css">
.callout {
margin-top: 1em;
margin-bottom: 1em;
border-radius: .25rem;
}
.callout.callout-style-simple {
padding: 0em 0.5em;
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
display: flex;
}
.callout.callout-style-default {
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
}
.callout .callout-body-container {
flex-grow: 1;
}
.callout.callout-style-simple .callout-body {
font-size: 1rem;
font-weight: 400;
}
.callout.callout-style-default .callout-body {
font-size: 0.9rem;
font-weight: 400;
}
.callout.callout-titled.callout-style-simple .callout-body {
margin-top: 0.2em;
}
.callout:not(.callout-titled) .callout-body {
display: flex;
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.callout:not(.no-icon).callout-titled.callout-style-simple .callout-content {
padding-left: 1.6em;
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.callout.callout-titled .callout-header {
padding-top: 0.2em;
margin-bottom: -0.2em;
}
.callout.callout-titled .callout-title p {
margin-top: 0.5em;
margin-bottom: 0.5em;
}
.callout.callout-titled.callout-style-simple .callout-content p {
margin-top: 0;
}
.callout.callout-titled.callout-style-default .callout-content p {
margin-top: 0.7em;
}
.callout.callout-style-simple div.callout-title {
border-bottom: none;
font-size: .9rem;
font-weight: 600;
opacity: 75%;
}
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border-bottom: none;
font-weight: 600;
opacity: 85%;
font-size: 0.9rem;
padding-left: 0.5em;
padding-right: 0.5em;
}
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padding-left: 0.5em;
padding-right: 0.5em;
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height: 1rem;
width: 1rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 1rem 1rem;
}
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height: 0.9rem;
width: 0.9rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 0.9rem 0.9rem;
}
.callout-title {
display: flex
}
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margin-top: 1rem;
padding-right: .5rem;
}
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display: none !important;
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margin-bottom: 0.5rem;
}
.callout.callout-titled .callout-icon::before {
margin-top: .5rem;
padding-right: .5rem;
}
.callout:not(.callout-titled) .callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
/* Callout Types */
div.callout-note {
border-left-color: #4582ec !important;
}
div.callout-note .callout-icon::before {
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}
div.callout-note.callout-style-default .callout-title {
background-color: #dae6fb
}
div.callout-important {
border-left-color: #d9534f !important;
}
div.callout-important .callout-icon::before {
background-image: url('data:image/png;base64,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');
}
div.callout-important.callout-style-default .callout-title {
background-color: #f7dddc
}
div.callout-warning {
border-left-color: #f0ad4e !important;
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</head>
<body class="quarto-light">
<div class="reveal">
<div class="slides">
<section id="title-slide" class="quarto-title-block center">
<h1 class="title">Introduction to Biostatistics and Machine Learning</h1>
<div class="quarto-title-authors">
<div class="quarto-title-author">
<div class="quarto-title-author-name">
22th - 26th April 2024
</div>
</div>
</div>
</section>
<section>
<section id="welcome" class="title-slide slide level1 center">
<h1>Welcome</h1>
</section>
<section id="introduction-to-biostatistics-and-machine-learning" class="slide level2">
<h2>Introduction to Biostatistics and Machine Learning</h2>
<p><br><br></p>
<div class="columns">
<div class="column" style="width:60%;">
<ul>
<li>22th - 26th April 2024</li>
<li>BMC, Husargatan 3, Uppsala</li>
<li>Room: Trippelrummet: E10:1307/8/9</li>
</ul>
</div><div class="column" style="width:40%;">
<div class="quarto-figure quarto-figure-left">
<figure>
<p><img data-src="images/robot-alex-knight.jpg" width="391"></p>
<figcaption>Image by Alex Knigth</figcaption>
</figure>
</div>
</div>
</div>
</section>
<section id="about-us" class="slide level2">
<h2>About us</h2>
<p><br><br></p>
<div class="fragment">
<div class="columns">
<div class="column" style="width:60%;">
<ul>
<li><a href="https://nbis.se/about/staff/olga-dethlefsen/">Olga Dethlefsen</a></li>
<li><a href="https://nbis.se/about/staff/eva-freyhult/">Eva Freyhult</a></li>
<li><a href="https://nbis.se/about/staff/payam-emami/">Payam Emami</a></li>
<li><a href="https://nbis.se/about/staff/julie-lorent/">Julie Lorent</a></li>
<li><a href="https://nbis.se/about/staff/mungwan-hong/">Mun-Gwan Hong</a></li>
</ul>
<p><br><br></p>
<ul>
<li>NBIS: National Bioinformatics Infrastructure Sweden</li>
<li>SciLifeLab Bioinformatics Platform</li>
<li><a href="https://www.scilifelab.se/units/nbis/" class="uri">https://www.scilifelab.se/units/nbis/</a></li>
</ul>
</div><div class="column" style="width:40%;">
<p><img data-src="images/nbis.png" width="391"></p>
</div>
</div>
<p><br><br></p>
<!-- ## What about you? -->
<!-- Names and teams -->
</div>
</section>
<section id="what-about-you" class="slide level2">
<h2>What about you?</h2>
</section>
<section id="what-about-you-1" class="slide level2">
<h2>What about you?</h2>
<img data-src="welcome_files/figure-revealjs/unnamed-chunk-2-1.png" width="960" class="r-stretch quarto-figure-center"></section>
<section id="what-about-you-2" class="slide level2">
<h2>What about you?</h2>
<img data-src="welcome_files/figure-revealjs/unnamed-chunk-3-1.png" width="960" class="r-stretch quarto-figure-center"></section>
<section id="what-about-you-3" class="slide level2">
<h2>What about you?</h2>
<img data-src="welcome_files/figure-revealjs/unnamed-chunk-4-1.png" width="960" class="r-stretch quarto-figure-center"></section>
<section id="what-about-you-4" class="slide level2">
<h2>What about you?</h2>
<p><br><br></p>
<div class="columns">
<div class="column" style="width:40%;">
<div class="cell">
<div class="cell-output-display">
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<thead>
<tr class="header">
<th style="text-align: left;" data-quarto-table-cell-role="th">First Name</th>
<th style="text-align: left;" data-quarto-table-cell-role="th">University</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: left;">Bangzhuo</td>
<td style="text-align: left;">Uppsala Universitet</td>
</tr>
<tr class="even">
<td style="text-align: left;">Elzbieta</td>
<td style="text-align: left;">Naturhistoriska Riksmuseet</td>
</tr>
<tr class="odd">
<td style="text-align: left;">Anusha Thakkutte</td>
<td style="text-align: left;">Uppsala Universitet</td>
</tr>
<tr class="even">
<td style="text-align: left;">Sara</td>
<td style="text-align: left;">Umeå Universitet</td>
</tr>
<tr class="odd">
<td style="text-align: left;">Yassine</td>
<td style="text-align: left;">Uppsala Universitet</td>
</tr>
<tr class="even">
<td style="text-align: left;">Maximilian</td>
<td style="text-align: left;">Kungliga Tekniska Högskolan, KTH</td>
</tr>
<tr class="odd">
<td style="text-align: left;">Stefan</td>
<td style="text-align: left;">Chalmers</td>
</tr>
<tr class="even">
<td style="text-align: left;">Linnéa</td>
<td style="text-align: left;">Uppsala Universitet</td>
</tr>
<tr class="odd">
<td style="text-align: left;">Yonglong</td>
<td style="text-align: left;">Karolinska Institutet</td>
</tr>
<tr class="even">
<td style="text-align: left;">Subhamita</td>
<td style="text-align: left;">Umeå Universitet</td>
</tr>
</tbody>
</table>
</div>
</div>
</div><div class="column" style="width:10%;">
</div><div class="column" style="width:40%;">
<div class="cell">
<div class="cell-output-display">
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<tr class="header">
<th style="text-align: left;" data-quarto-table-cell-role="th">First Name</th>
<th style="text-align: left;" data-quarto-table-cell-role="th">University</th>
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<tbody>
<tr class="odd">
<td style="text-align: left;">Erik</td>
<td style="text-align: left;">Chalmers</td>
</tr>
<tr class="even">
<td style="text-align: left;">Agata</td>
<td style="text-align: left;">Chalmers</td>
</tr>
<tr class="odd">
<td style="text-align: left;">Vishnu</td>
<td style="text-align: left;">Umeå Universitet</td>
</tr>
<tr class="even">
<td style="text-align: left;">Sheng Leslie</td>
<td style="text-align: left;">Luleå university of technology</td>
</tr>
<tr class="odd">
<td style="text-align: left;">Anna</td>
<td style="text-align: left;">Radboud University, Nijmegen, NL</td>
</tr>
<tr class="even">
<td style="text-align: left;">Raphaël</td>
<td style="text-align: left;">Kungliga Tekniska Högskolan, KTH</td>
</tr>
<tr class="odd">
<td style="text-align: left;">Gustav</td>
<td style="text-align: left;">Karolinska Institutet</td>
</tr>
<tr class="even">
<td style="text-align: left;">Nils</td>
<td style="text-align: left;">Sveriges lantbruksuniversitet, SLU</td>
</tr>
<tr class="odd">
<td style="text-align: left;">Yuan</td>
<td style="text-align: left;">Lund Universitet</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
</section></section>
<section>
<section id="practicalities" class="title-slide slide level1 center">
<h1>Practicalities</h1>
</section>
<section id="room" class="slide level2">
<h2>Room</h2>
<p><br><br></p>
<div class="fragment">
<div class="columns">
<div class="column" style="width:60%;">
<div>
<ul>
<li class="fragment">same room entire week</li>
<li class="fragment">please drink coffee and eat snacks outside</li>
<li class="fragment">bathrooms locations</li>
<li class="fragment">no access cards to the building (apologies!)</li>
<li class="fragment">we will lock the room when going for lunch</li>
<li class="fragment">lunch: Monday, Tuesday, Thursday and Friday at Bikupan</li>
<li class="fragment">lunch: Wednesday at Sven Dufva</li>
</ul>
</div>
</div><div class="column" style="width:40%;">
<div class="quarto-figure quarto-figure-left">
<figure>
<p><img data-src="images/robot-andrea-de-santis.jpg" width="291"></p>
<figcaption>Image by Andrea de Santis</figcaption>
</figure>
</div>
</div>
</div>
</div>
</section>
<section id="internet" class="slide level2">
<h2>Internet</h2>
<p><br><br></p>
<div class="columns">
<div class="column" style="width:60%;">
<ul>
<li>Eduroam</li>
<li>WiFi network UU-Guest</li>
</ul>
</div><div class="column" style="width:40%;">
<div class="quarto-figure quarto-figure-left">
<figure>
<p><img data-src="images/wifi.png" width="200"></p>
</figure>
</div>
</div>
</div>
</section>
<section id="course-website" class="slide level2">
<h2>Course website</h2>
<p><br><br></p>
<div>
<ul>
<li class="fragment"><a href="https://uppsala.instructure.com/courses/93277" class="uri">https://uppsala.instructure.com/courses/93277</a></li>
<li class="fragment">you should be now enrolled and be able to access materials incl. quizzes</li>
</ul>
</div>
</section>
<section id="canvas-demo" class="slide level2">
<h2>Canvas Demo</h2>
<p><br><br></p>
<ul>
<li>Schedule</li>
<li>Modules</li>
<li>Chat</li>
<li>Discussion</li>
<li>Files</li>
<li>Announcements</li>
<li>Quiz</li>
</ul>
<p><em>please change your name under the Profile</em></p>
<p><br><br></p>
</section>
<section id="certificate-requirements" class="slide level2">
<h2>Certificate requirements</h2>
<p><br><br></p>
<div class="columns">
<div class="column" style="width:60%;">
<div class="fragment fade-in">
<ol type="1">
<li>presence in all sessions during the week
<ul>
<li>we may allow skipping up to 4h during the week</li>
</ul></li>
</ol>
</div>
<div class="fragment fade-in">
<ol start="2" type="1">
<li>completing “Daily challenge” quiz
<ul>
<li>opens daily at 15.00</li>
<li>closes at 09:00 the following day</li>
</ul></li>
</ol>
</div>
<div class="fragment fade-in">
<ol start="3" type="1">
<li>active participation during the week</li>
</ol>
</div>
</div><div class="column" style="width:40%;">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/certificate.png" width="200"></p>
</figure>
</div>
</div>
</div>
<div class="fragment">
<p><em>Note that we are not able to provide any formal university credits (högskolepoäng). Many universities, however, recognize the attendance in our courses, and award 1.5 HPs, corresponding to 40h of studying. It is up to participants to clarify and arrange credit transfer with the relevant university department.</em></p>
<p><br><br></p>
</div>
</section>
<section id="payams-active-participation-rule" class="slide level2">
<h2>Payam’s Active Participation rule</h2>
<p><br><br></p>
<div class="fragment">
<div class="columns">
<div class="column" style="width:70%;">
<div class="fragment fade-in">
<ol type="1">
<li>there are no wrong answers</li>
</ol>
</div>
<div class="fragment fade-in">
<ol start="2" type="1">
<li>except: “I do not know” or its equivalents</li>
</ol>
</div>
<div class="fragment fade-in">
<ol start="3" type="1">
<li>so when asked a question, say something because 1.</li>
</ol>
</div>
</div><div class="column" style="width:30%;">
<div class="quarto-figure quarto-figure-left">
<figure>
<p><img data-src="images/robot-hand.jpg" width="191"></p>
<figcaption>Image by <span class="citation" data-cites="thisisengineering">@thisisengineering</span></figcaption>
</figure>
</div>
</div>
</div>
</div>
<div class="fragment">
<p><strong>Help us building a stimulating learning environment</strong> by actively participating. We love when you talk and ask questions!</p>
</div>
</section>
<section id="not-enough-time" class="slide level2">
<h2>Not enough time</h2>
<p><br><br></p>
<div class="columns">
<div class="column" style="width:70%;">
<p>There is (probably) not enough time during the course to complete all the exercises.</p>
<ul>
<li>It may be good to prioritize.</li>
<li>We can schedule a follow-up online session.</li>
<li>We will come back to this on Friday.</li>
</ul>
</div><div class="column" style="width:30%;">
<div class="quarto-figure quarto-figure-left">
<figure>
<p><img data-src="images/DALLE-time-03.png" width="291"></p>
<figcaption>generated by DALL <span class="math inline">\(\cdot\)</span> E 2</figcaption>
</figure>
</div>
</div>
</div>
</section></section>
<section>
<section id="course-background-aim" class="title-slide slide level1 center">
<h1>Course: background & aim</h1>
</section>
<section id="background" class="slide level2">
<h2>Background</h2>
<p><br><br></p>
<div class="fragment">
<div class="columns">
<div class="column" style="width:60%;">
<p><em>“If you torture the data long enough, it will confess to anything”</em></p>
<p><em>Ronald Coase, British Economist</em></p>
</div><div class="column" style="width:10%;">
</div><div class="column" style="width:30%;">
<div class="quarto-figure quarto-figure-left">
<figure>
<p><img data-src="images/bell-curve.png" width="300"></p>
<figcaption>image by Richa Bhatia</figcaption>
</figure>
</div>
</div>
</div>
</div>
</section>
<section id="background-1" class="slide level2">
<h2>Background</h2>
<p><br><br></p>
<div class="columns">
<div class="column" style="width:60%;">
<p>Some common problems we have been observing are due to:</p>
<div>
<ul>
<li class="fragment">incorrect study design e.g. absence of adequate controls</li>
<li class="fragment">forming incorrectly null and alternative hypothesis</li>
<li class="fragment">applying statistical methods without understanding</li>
<li class="fragment">misinterpreting the output of the statistical methods</li>
<li class="fragment">circular analysis, e.g. testing hypotheses on same sample that led to the generation of the hypotheses in the first place</li>
</ul>
</div>
</div><div class="column" style="width:10%;">
</div><div class="column" style="width:30%;">
<div class="quarto-figure quarto-figure-left">
<figure>
<p><img data-src="images/bell-curve.png" width="300"></p>
<figcaption>image by Richa Bhatia</figcaption>
</figure>
</div>
</div>
</div>
<!-- ## Background -->
<!-- <br/><br/> -->
<!-- . . . -->
<!-- *"Today, of course, we have high-speed computers and prepackaged statistical routines to perform the necessary calculations.* ***Yet, statistical software will no more make one a statistician than would a scalpel turn one into a neurosurgeon.*** *Allowing these tools to do our thinking for us is a sure recipe for disaster."* -->
<!-- *from Common Errors in Statistics (and How to Avoid Them) by Philip I. Good and James W. Hardin* -->
</section>
<section id="aim" class="slide level2">
<h2>Aim</h2>
<p><br><br></p>
<div class="fragment">
<p>We aim to <strong>focus on fundamentals</strong> since we believe that getting the basics right will help with:</p>
<ul>
<li>avoiding common errors &</li>
<li>studying more advanced topics.</li>
</ul>
</div>
</section>
<section id="aim-1" class="slide level2">
<h2>Aim</h2>
<div class="columns">
<div class="column" style="width:50%;">
<p><strong>What do we want you to gain from this course?</strong></p>
<div class="fragment fade-in">
<ul>
<li>Framework for statistical learning: learn a selection of method & develop an understanding to apply methods correctly and explore them independently</li>
</ul>
</div>
<div class="fragment fade-in">
<ul>
<li>Appreciation of theory incl. not being afraid of equations</li>
</ul>
<!-- $$x^2 + \left ( \frac{5y}{4}-\sqrt{|x|} \right )^2 = 1$$ -->
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="welcome_files/figure-revealjs/unnamed-chunk-7-1.png" width="432"></p>
</figure>
</div>
</div>
</div>
</div>
</div><div class="column" style="width:10%;">
</div><div class="column" style="width:40%;">
<p><strong>How?</strong></p>
<div class="fragment fade-in">
<ul>
<li>We will look in detail into selected methods</li>
</ul>
</div>
<div class="fragment fade-in">
<ul>
<li>Over the week we will build up our understanding of different aspects of a typical data analysis project and demonstrate how to combine all the steps to build a predictive model.</li>
</ul>
</div>
</div>
</div>
</section></section>
<section>
<section id="course-content" class="title-slide slide level1 center">
<h1>Course Content</h1>
</section>
<section id="content" class="slide level2">
<h2>Content</h2>
<div class="fragment">
<p><br><br></p>
<p><em>Let’s consider some common cases…</em></p>
</div>
</section>
<section id="content-1" class="slide level2">
<h2>Content</h2>
<div class="fragment">
<p><br><br></p>
<p><strong>Case 1: Mouse Knockout Experiment</strong></p>
</div>
</section>
<section id="content-mouse-knockout-experiment" class="slide level2">
<h2>Content: Mouse Knockout Experiment</h2>
<p><em>Case 1: Mouse Knockout Experiment</em></p>
<p><em>Does LDL receptor gene affect the total plasma cholesterol?</em></p>
<div class="fragment">
<p><br><br></p>
<div class="columns">
<div class="column" style="width:50%;">
<h3 id="setup">Setup</h3>
<p>We have access to data from an experiment:</p>
<ul>
<li>10 wild type (WT) mice</li>
<li>10 LDLR knockout (KO) mice</li>
</ul>
<p>where plasma concentration of total cholesterol was measured at one time point after feeding on high fat diet</p>
</div><div class="column" style="width:10%;">
</div><div class="column" style="width:40%;">
<div class="quarto-figure quarto-figure-left">
<figure>
<p><img data-src="images/DALLE-mice.png" width="291"></p>
<figcaption>generated by DALL <span class="math inline">\(\cdot\)</span> E 2</figcaption>
</figure>
</div>
</div>
</div>
</div>
</section>
<section id="content-mouse-knockout-experiment-1" class="slide level2">
<h2>Content: Mouse Knockout Experiment</h2>
<p><br><br></p>
<h3 id="visualize-results">Visualize results</h3>
<div class="columns">
<div class="column" style="width:40%;">
<div class="cell">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="welcome_files/figure-revealjs/mice-scatter-1.png" width="864"></p>
</figure>
</div>
</div>
</div>
</div><div class="column" style="width:10%;">
</div><div class="column" style="width:40%;">
<div class="fragment fade-in">
<ul>
<li>Not so informative.</li>
</ul>
</div>
<div class="fragment fade-in">
<ul>
<li>Let’s improve!</li>
</ul>
</div>
</div>
</div>
</section>
<section id="content-mouse-knockout-experiment-2" class="slide level2">
<h2>Content: Mouse Knockout Experiment</h2>
<p><br><br></p>
<div class="columns">
<div class="column" style="width:40%;">
<div class="cell">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="welcome_files/figure-revealjs/mice-boxplot-1.png" width="864"></p>
</figure>
</div>
</div>
</div>
</div><div class="column" style="width:10%;">
</div><div class="column" style="width:40%;">
<div class="fragment fade-in">
<!-- -->
<h3 id="improved-visualization">Improved visualization</h3>
</div>
<div class="fragment fade-in">
<ul>
<li>Collect KO and WT separately as columns in a box plot</li>
</ul>
</div>
<div class="fragment fade-in">
<ul>
<li>Visualize <strong>distribution</strong> of sample values using <strong>descriptive statistics</strong> such as median and quartiles</li>
</ul>
</div>
<div class="fragment fade-in">
<div class="fragment highlight-blue">
<!-- -->
<h3 id="we-will-talk-more">We will talk more:</h3>
<ul>
<li>exploratory data analysis</li>
<li>summarizing data with descriptive statistics</li>
<li>visualizing data</li>
</ul>
</div>
</div>
</div>
</div>
<!-- Interpretation -->
</section>
<section id="content-mouse-knockout-experiment-3" class="slide level2">
<h2>Content: Mouse Knockout Experiment</h2>
<p><br><br></p>
<div class="columns">
<div class="column" style="width:40%;">
<div class="cell">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="welcome_files/figure-revealjs/mice-boxplot-again-1.png" width="864"></p>
</figure>
</div>
</div>
</div>
</div><div class="column" style="width:10%;">
</div><div class="column" style="width:50%;">
<h3 id="interpretation">Interpretation</h3>
<div class="fragment fade-in">
<ul>
<li>Intuitively, there is a <strong>clear difference</strong> between KO and WT based on the box plot</li>
</ul>
</div>
</div>
</div>
</section>
<section id="content-mouse-knockout-experiment-4" class="slide level2">
<h2>Content: Mouse Knockout Experiment</h2>
<p><br><br></p>
<div class="columns">
<div class="column" style="width:40%;">
<div class="cell">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="welcome_files/figure-revealjs/mice-boxplot-no-difference-1.png" width="864"></p>
</figure>
</div>
</div>
</div>
</div><div class="column" style="width:10%;">
</div><div class="column" style="width:50%;">
<h3 id="interpretation-1">Interpretation</h3>
<div class="fragment fade-in">
<ul>
<li>Intuitively, there is <strong>no difference</strong> between KO and WT based on the box plot</li>
</ul>
</div>
</div>
</div>
</section>
<section id="content-mouse-knockout-experiment-5" class="slide level2">
<h2>Content: Mouse Knockout Experiment</h2>
<p><br><br></p>
<div class="columns">
<div class="column" style="width:40%;">
<div class="cell">
<div class="cell-output-display">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="welcome_files/figure-revealjs/mice-boxplot-less-difference-1.png" width="864"></p>