DEseq2 design for additive treatment

<html> <head> <title> DEseq2 design for additive treatment </title> <meta charset="UTF-8"> <meta name="viewport" content="width=device-width, initial-scale=1"> <link rel="icon" href="/static/favicon.ico" type="image/x-icon"/> <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script> <script async src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js" id="MathJax-script"></script> <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script> <script src="https://code.jquery.com/ui/1.12.1/jquery-ui.min.js"></script> <link disabled rel="stylesheet" href="//cdn.jsdelivr.net/gh/highlightjs/cdn-release@9.18.0/build/styles/default.min.css"> <script async src="//cdn.jsdelivr.net/gh/highlightjs/cdn-release@9.18.0/build/highlight.min.js"></script>  <script async src="https://www.googletagmanager.com/gtag/js?id=UA-55275703-1"></script> <script> window.dataLayer = window.dataLayer || []; function gtag() { dataLayer.push(arguments); } 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icon"></i>About </a> </div> </div> </div> </span> <div class="ui bottom attached segment block"> <div class="ui stackable grid"> <div class="fit twelve wide content column"> <span itemprop="mainEntity" itemscope itemtype="https://schema.org/Question"> <div class="ui vertical segment"> <a name="9161344"></a> <div class="post view open" data-value="9161344"> <div class="title" itemprop="name">DEseq2 design for additive treatment</div> <span itemprop="answerCount" style="display: none">1</span> <div class="body" > <div class="voting"> <button class="ui icon button" data-value="upvote" data-state="0"><i class="thumbs up icon"></i> </button> <div class="score" itemprop="upvoteCount">0</div> <button class="ui icon button" data-value="bookmark" data-state="0"><i class="bookmark icon"></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="wrap magnify"> <div class="user_box tablet right"> <div> <a class="" href="/u/14806/"> <img class="ui centered circular image" src="https://secure.gravatar.com/avatar/25050ecdf8533e345004931231339cc3?s=80&d=mp"> </a> </div> <div class="muted"> <div><a href="/u/14806/">picasa1983</a> • 0 </div> @picasa1983-14806 <div>Last seen 6 hours ago</div> <div>USA</div> </div> </div> <span itemprop="text"> <p>Hi,</p> <p>I have a single factor (Treatment), three levels (Drug1, Drug2, Drug3)</p> <pre><code>dds <- DESeqDataSetFromMatrix(data, colData, design = ~ Treatment) dds <- DESeq(dds) results = results(dds) </code></pre> <p>If I want to get the DEG for Drug1 vs Drug2, I do:</p> <pre><code>results = results(dds, contrast = c("Treatment" , "Drug1" , "Drug2")) </code></pre> <p>Drug2 vs Drug3, I do:</p> <pre><code>results = results(dds, contrast = c("Treatment" , "Drug2" , "Drug3")) </code></pre> <p>But how to do Drug1 vs (Drug2 + Drug3) ?</p> <p>Should I create a new factor (ex: MixTreatment) with 2 levels Drug1, DrugMix = (Drug2 + Drug3) and then do:</p> <pre><code>results = results(dds, contrast = c("MixTreatment" , "DrugMix")) </code></pre> <p>or alternative approach ?</p> <p>Thanks,</p> </span> </div> <span class="inplace-tags"> <a class="ptag" href="/tag/DESeq2/"> DESeq2 </a> • 177 views </span> <time itemprop="dateCreated" datetime="2025-02-23"></time> <div class="actions top-level"> <a class="add-comment ui tiny label">ADD COMMENT</a> • <a itemprop="url" href="/p/9161344/#9161344">link</a> <span class="status muted user-info"> updated 1 day ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/13662/"> <span itemprop="name">ATpoint</span> </a> &starf; 4.7k • written 2 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/14806/"> <span itemprop="name">picasa1983</span> </a> • 0 </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> <div class="ui vertical segment"> <a name="9161345"></a> <div class="post view open" data-value="9161345"> <div class="body" itemprop="suggestedAnswer" itemscope itemtype="https://schema.org/Answer" > <div class="voting"> <button class="ui icon button" data-value="upvote" data-state="0"><i class="thumbs up icon"></i> </button> <div class="score" itemprop="upvoteCount">1</div> <button class="ui icon button" data-value="bookmark" data-state="0"><i class="bookmark icon"></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="wrap magnify"> <div class="user_box tablet right"> <div> <a class="" href="/u/13662/"> <img class="ui centered circular image" src="https://secure.gravatar.com/avatar/f08050345f8a0ff11e9bbaab4a1c4212?s=80&d=retro"> </a> </div> <div class="muted"> <div><a href="/u/13662/">ATpoint</a> &starf; 4.7k </div> @atpoint-13662 <div>Last seen 8 hours ago</div> <div>Germany</div> </div> </div> <span itemprop="text"> <p>See <a href="https://support.bioconductor.org/p/69104/#69197" rel="nofollow">DESeq2: Compare expression of one group to the mean of others</a>, <a href="https://support.bioconductor.org/p/129755/" rel="nofollow">DESeq2: Comparing one sample with the mean of all</a> for testing against an average. Many other threads if searching for "deseq2 test average".</p> </span> </div> <time itemprop="dateCreated" datetime="2025-02-24"></time> <div class="actions "> <a class="add-comment ui tiny label">ADD COMMENT</a> • <a itemprop="url" href="/p/9161344/#9161345">link</a> <span class="status muted user-info"> <span> 1 day ago <a href="/u/13662/"> ATpoint </a> &starf; 4.7k </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> </span> <div class="ui info message"> <p><a class="ui small label" href="/accounts/login/"> <i class="sign in icon"></i>Login</a> before adding your answer.</p> </div> <script> $(document).ready(function () { $('#subscribe').dropdown(); drag_and_drop(); $('.ui.dropdown').dropdown(); //var users = "**MISSING**".split(','); autocomplete_users(); //init_pagedown(); $(this).on('click', '#inplace .save', function () { event.preventDefault(); var post = $(this).closest('.post'); edit_dropdown_post(post); }); $(this).on('click', '#inplace .create', function () { event.preventDefault(); create_comment(); }); $(this).on('click', '.edit-button', function (event) { event.preventDefault(); inplace_form($(this)); }); $(this).on('click', ".add-comment", function () { inplace_form($(this), true); }); }); </script> </div> <div class="four wide column sidefeed"> <div class="ui large wrap-text" id="sidebar"> <div class="ui large wrap-text" id="sidebar"> <div class="title">Similar Posts</div> <div class="ui basic segment similar" id="similar"> <div id="similar-feed" post_uid="9161344"></div> <div class="ui inverted dimmer"> <div class="content"> <div class="ui text loader"> <div class="muted">Loading Similar Posts</div> </div> </div> </div> </div> </div> </div> </div> </div> <div id="traffic">Traffic: 623 users visited in the last hour</div> </div> <div class="ui three center aligned column stackable tiny grid"> <div class=" left aligned column" style="padding-right: 13%"> <b>Content</b> <a href="/#search-anchor">Search</a><br> <a href="/user/list/">Users</a><br> <a href="/t/">Tags</a><br> <a href="/b/list/">Badges</a> </div> <div class="left aligned column" style="padding-right: 12%"> <b>Help</b> <a href="/info/about/">About</a><br> <a href="/info/faq/">FAQ</a><br> </div> <div class=" left aligned column"> <b>Access</b> <a href="/info/rss/">RSS</a><br> <a href="/info/api/">API</a><br> <a href="#">Stats</a> </div> </div> <div class="ui divider"></div> <div class="ui vertical center aligned basic segment"> <p>Use of this site constitutes acceptance of our <a href="/info/policy/">User Agreement and Privacy Policy</a>.</p> <div class="smaller muted"> Powered by the <a href="https://github.com/ialbert/biostar-central" class="ui image"> <img src="/static/images/badge-forum.svg"></a> version 2.3.6 </div> </div> </div> </body> </html>

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DEseq2 design for additive treatment