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            <h1 id="seo-header">【迁移】Counts矩阵的标准化方法：TMM和VST、RLOG</h1>
            
              <p id="updated-time" class="note note-info" style="">
                
                  
                    Last updated on March 19, 2024 pm
                  
                
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                <ul>
<li><a target="_blank" rel="noopener" href="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-3-r25">TMM</a>：The Trimmed Mean of M value by edgeR</li>
<li><a target="_blank" rel="noopener" href="http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html">VST</a>：The variance stabilizing transformation by DESeq2</li>
<li><a target="_blank" rel="noopener" href="http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html">RLOG</a>：The regularized-logarithm transformation by DESeq2</li>
</ul>
<p>Counts矩阵来源于<a href="/STAR--yi-jian-jiao-ben">STAR匹配得到的结果</a>：<code>df &lt;- read.csv('GSE123379.csv', row.names = 1)</code></p>
<h2 id="安装补充包">安装补充包</h2>
<ul>
<li><a href="/cong-cha-yi-ji-yin-dao-RRA-ju-he">conda activate tcga</a></li>
<li>conda install -c bioconda bioconductor-edger -y</li>
</ul>
<h2 id="TMM方法">TMM方法</h2>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br></pre></td><td class="code"><pre><span class="line">f_counts2TMM <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>countsMatrix<span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    require<span class="punctuation">(</span>edgeR<span class="punctuation">)</span></span><br><span class="line">    TMM <span class="operator">&lt;-</span> DGEList<span class="punctuation">(</span>counts <span class="operator">=</span> countsMatrix<span class="punctuation">)</span></span><br><span class="line">    TMM <span class="operator">&lt;-</span> calcNormFactors<span class="punctuation">(</span>TMM<span class="punctuation">,</span> method <span class="operator">=</span> <span class="string">&#x27;TMM&#x27;</span><span class="punctuation">)</span></span><br><span class="line">    cpm<span class="punctuation">(</span>TMM<span class="punctuation">,</span> normalized.lib.sizes <span class="operator">=</span> <span class="literal">TRUE</span><span class="punctuation">,</span> <span class="built_in">log</span><span class="operator">=</span><span class="built_in">F</span><span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">countsMatrix <span class="operator">&lt;-</span> df<span class="punctuation">[</span><span class="operator">-</span><span class="punctuation">(</span><span class="number">1</span><span class="operator">:</span><span class="number">3</span><span class="punctuation">)</span><span class="punctuation">]</span></span><br><span class="line">TMM <span class="operator">&lt;-</span> f_counts2TMM<span class="punctuation">(</span>countsMatrix<span class="punctuation">)</span></span><br><span class="line">TMM</span><br></pre></td></tr></table></figure>
<h2 id="VST方法">VST方法</h2>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br></pre></td><td class="code"><pre><span class="line">f_counts2VST <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>countsMatrix<span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    require<span class="punctuation">(</span>DESeq2<span class="punctuation">)</span></span><br><span class="line">    conditions <span class="operator">&lt;-</span> factor<span class="punctuation">(</span><span class="built_in">rep</span><span class="punctuation">(</span><span class="string">&quot;Control&quot;</span><span class="punctuation">,</span>ncol<span class="punctuation">(</span>countsMatrix<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">    colData_b <span class="operator">&lt;-</span> data.frame<span class="punctuation">(</span>row.names <span class="operator">=</span> colnames<span class="punctuation">(</span>countsMatrix<span class="punctuation">)</span><span class="punctuation">,</span> conditions<span class="punctuation">)</span></span><br><span class="line">    dds <span class="operator">&lt;-</span> DESeqDataSetFromMatrix<span class="punctuation">(</span>countData <span class="operator">=</span> countsMatrix<span class="punctuation">,</span></span><br><span class="line">                              colData <span class="operator">=</span> colData_b<span class="punctuation">,</span></span><br><span class="line">                              design <span class="operator">=</span> <span class="operator">~</span> <span class="number">1</span><span class="punctuation">)</span></span><br><span class="line">    vsd <span class="operator">&lt;-</span> vst<span class="punctuation">(</span>object<span class="operator">=</span>dds<span class="punctuation">,</span> blind<span class="operator">=</span><span class="built_in">T</span><span class="punctuation">)</span> </span><br><span class="line">    assay<span class="punctuation">(</span>vsd<span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">countsMatrix <span class="operator">&lt;-</span> df<span class="punctuation">[</span><span class="operator">-</span><span class="punctuation">(</span><span class="number">1</span><span class="operator">:</span><span class="number">3</span><span class="punctuation">)</span><span class="punctuation">]</span></span><br><span class="line">VST <span class="operator">&lt;-</span> f_counts2VST<span class="punctuation">(</span>countsMatrix<span class="punctuation">)</span></span><br><span class="line">VST</span><br></pre></td></tr></table></figure>
<h2 id="RLOG方法">RLOG方法</h2>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br></pre></td><td class="code"><pre><span class="line">f_counts2RLOG <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>countsMatrix<span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">    require<span class="punctuation">(</span>DESeq2<span class="punctuation">)</span></span><br><span class="line">    conditions <span class="operator">&lt;-</span> factor<span class="punctuation">(</span><span class="built_in">rep</span><span class="punctuation">(</span><span class="string">&quot;Control&quot;</span><span class="punctuation">,</span>ncol<span class="punctuation">(</span>countsMatrix<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">    colData_b <span class="operator">&lt;-</span> data.frame<span class="punctuation">(</span>row.names <span class="operator">=</span> colnames<span class="punctuation">(</span>countsMatrix<span class="punctuation">)</span><span class="punctuation">,</span> conditions<span class="punctuation">)</span></span><br><span class="line">    dds <span class="operator">&lt;-</span> DESeqDataSetFromMatrix<span class="punctuation">(</span>countData <span class="operator">=</span> countsMatrix<span class="punctuation">,</span></span><br><span class="line">                              colData <span class="operator">=</span> colData_b<span class="punctuation">,</span></span><br><span class="line">                              design <span class="operator">=</span> <span class="operator">~</span> <span class="number">1</span><span class="punctuation">)</span></span><br><span class="line">    rld  <span class="operator">&lt;-</span> rlog<span class="punctuation">(</span>object<span class="operator">=</span>dds<span class="punctuation">,</span> blind<span class="operator">=</span><span class="built_in">T</span><span class="punctuation">)</span> </span><br><span class="line">    assay<span class="punctuation">(</span>rld<span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">countsMatrix <span class="operator">&lt;-</span> df<span class="punctuation">[</span><span class="operator">-</span><span class="punctuation">(</span><span class="number">1</span><span class="operator">:</span><span class="number">3</span><span class="punctuation">)</span><span class="punctuation">]</span></span><br><span class="line">RLOG <span class="operator">&lt;-</span> f_counts2RLOG<span class="punctuation">(</span>countsMatrix<span class="punctuation">)</span></span><br><span class="line">RLOG</span><br></pre></td></tr></table></figure>
                
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