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            <h1 id="seo-header">【迁移】oligo：GEO/ArrayExpress芯片数据处理</h1>
            
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                    Last updated on March 19, 2024 pm
                  
                
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                <h2 id="安装依赖">安装依赖</h2>
<figure class="highlight bash"><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><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br></pre></td><td class="code"><pre><code class="hljs bash">conda clean -y -all<br>conda create -n geo -c conda-forge r-base=4.1.3<br>conda activate geo<br>conda install -c conda-forge r-tidyverse=1.3.1 -y<br>conda install -c conda-forge r-irkernel -y<br>conda install -c conda-forge r-r.utils -y<br>conda install -c conda-forge r-rcolorbrewer -y<br>Rscript -e <span class="hljs-string">&quot;IRkernel::installspec(name=&#x27;geo&#x27;, displayname=&#x27;r-geo&#x27;)&quot;</span><br>conda install -c bioconda bioconductor-geoquery -y<br>conda install -c bioconda bioconductor-oligo -y<br>conda install -c bioconda bioconductor-affy -y<br>conda install -c bioconda bioconductor-pd.hugene.1.0.st.v1 -y <span class="hljs-comment"># read.celfiles 需要啥安装啥</span><br>conda install -c bioconda bioconductor-pd.hg.u133a.2 -y<br>conda install -c bioconda bioconductor-arrayexpress -y<br>conda install -c bioconda bioconductor-biomart -y<br>conda install -c bioconda bioconductor-affycoretools -y<br></code></pre></td></tr></table></figure>
<h2 id="下载芯片数据">下载芯片数据</h2>
<h3 id="GEO">GEO</h3>
<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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>GEOquery<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>oligo<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>affy<span class="hljs-punctuation">)</span><br>gse<span class="hljs-operator">=</span><span class="hljs-string">&quot;GSE43332&quot;</span><br>rawdata <span class="hljs-operator">&lt;-</span> getGEOSuppFiles<span class="hljs-punctuation">(</span>gse<span class="hljs-punctuation">)</span> <span class="hljs-comment">#下载原始数据</span><br>rawdata<br>setwd<span class="hljs-punctuation">(</span>gse<span class="hljs-punctuation">)</span><br>untar<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;GSE43332_RAW.tar&quot;</span><span class="hljs-punctuation">,</span>exdir <span class="hljs-operator">=</span> <span class="hljs-string">&quot;.&quot;</span><span class="hljs-punctuation">)</span><br>celfiles <span class="hljs-operator">&lt;-</span> list.files<span class="hljs-punctuation">(</span>pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;*CEL.gz$&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-comment">#批量查找并列出后缀为.gz的文件</span><br>data.raw <span class="hljs-operator">&lt;-</span> read.celfiles<span class="hljs-punctuation">(</span>celfiles<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h3 id="ArrayExpress">ArrayExpress</h3>
<ul>
<li>~/dev/xray/xray -c ~/etc/xui2.json &amp;</li>
<li>wget -e “https_proxy=<a href="https://hexo.limour.top/go/#aHR0cDovLzEyNy4wLjAuMToyMDgwOQ==" rel="noopener external nofollow noreferrer">http://127.0.0.1:20809</a>” <a href="https://hexo.limour.top/go/#aHR0cHM6Ly93d3cuZWJpLmFjLnVrL2FycmF5ZXhwcmVzcy9maWxlcy9FLU1FWFAtMTQyMi9FLU1FWFAtMTQyMi5yYXcuMS56aXA=" rel="noopener external nofollow noreferrer">https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-1422/E-MEXP-1422.raw.1.zip</a> -O E-MEXP-1422.raw.1.zip</li>
<li>unzip E-MEXP-1422.raw.1.zip</li>
</ul>
<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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>ArrayExpress<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>oligo<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>affy<span class="hljs-punctuation">)</span><br><span class="hljs-comment"># Sys.setenv(&quot;http_proxy&quot;=&quot;http://127.0.0.1:20809&quot;)</span><br><span class="hljs-comment"># Sys.setenv(&quot;https_proxy&quot;=&quot;http://127.0.0.1:20809&quot;)</span><br><span class="hljs-comment"># mexp1422=getAE(&quot;E-MTAB-6128&quot;, type = &#x27;raw&#x27;, extract = T)</span><br>celfiles <span class="hljs-operator">&lt;-</span> list.files<span class="hljs-punctuation">(</span>pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;*.CEL$&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-comment">#批量查找并列出后缀为CEL的文件</span><br>data.raw <span class="hljs-operator">&lt;-</span> read.celfiles<span class="hljs-punctuation">(</span>celfiles<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h2 id="RMA标准化数据">RMA标准化数据</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><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br></pre></td><td class="code"><pre><code class="hljs R">sampleNames<span class="hljs-punctuation">(</span>data.raw<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> sapply<span class="hljs-punctuation">(</span>strsplit<span class="hljs-punctuation">(</span>sampleNames<span class="hljs-punctuation">(</span>data.raw<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;_&quot;</span><span class="hljs-punctuation">,</span>fixed<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;[&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>sampleNames<span class="hljs-punctuation">(</span>data.raw<span class="hljs-punctuation">)</span><br> <br>fit1 <span class="hljs-operator">&lt;-</span> fitProbeLevelModel<span class="hljs-punctuation">(</span>data.raw<span class="hljs-punctuation">)</span><br> <br>image<span class="hljs-punctuation">(</span>fit1<span class="hljs-punctuation">,</span>type<span class="hljs-operator">=</span><span class="hljs-string">&quot;weights&quot;</span><span class="hljs-punctuation">,</span>which<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>main<span class="hljs-operator">=</span><span class="hljs-string">&quot;weights&quot;</span><span class="hljs-punctuation">)</span><br>image<span class="hljs-punctuation">(</span>fit1<span class="hljs-punctuation">,</span>type<span class="hljs-operator">=</span><span class="hljs-string">&quot;residuals&quot;</span><span class="hljs-punctuation">,</span>which<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>main<span class="hljs-operator">=</span><span class="hljs-string">&quot;Residuals&quot;</span><span class="hljs-punctuation">)</span><br>image<span class="hljs-punctuation">(</span>fit1<span class="hljs-punctuation">,</span>type<span class="hljs-operator">=</span><span class="hljs-string">&quot;sign.residuals&quot;</span><span class="hljs-punctuation">,</span>which<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>main<span class="hljs-operator">=</span><span class="hljs-string">&quot;Residuals.sign&quot;</span><span class="hljs-punctuation">)</span><br> <br>data.eset <span class="hljs-operator">&lt;-</span> oligo<span class="hljs-operator">::</span>rma<span class="hljs-punctuation">(</span>data.raw<span class="hljs-punctuation">)</span><br>data.exprs <span class="hljs-operator">&lt;-</span> exprs<span class="hljs-punctuation">(</span>data.eset<span class="hljs-punctuation">)</span><br> <br>library<span class="hljs-punctuation">(</span>RColorBrewer<span class="hljs-punctuation">)</span><br>display.brewer.all<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br><span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>ncol<span class="hljs-punctuation">(</span>data.eset<span class="hljs-punctuation">)</span><span class="hljs-operator">&gt;</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    colors <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>brewer.pal<span class="hljs-punctuation">(</span><span class="hljs-number">8</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;Set2&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>brewer.pal<span class="hljs-punctuation">(</span>ncol<span class="hljs-punctuation">(</span>data.eset<span class="hljs-punctuation">)</span><span class="hljs-operator">-</span><span class="hljs-number">8</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;Set1&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>    colors <span class="hljs-operator">&lt;-</span> brewer.pal<span class="hljs-punctuation">(</span>ncol<span class="hljs-punctuation">(</span>data.eset<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;Set2&quot;</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>boxplot<span class="hljs-punctuation">(</span>data.exprs<span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span>colors<span class="hljs-punctuation">,</span>main<span class="hljs-operator">=</span><span class="hljs-string">&quot;afterRMA&quot;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h2 id="探针转Symbol">探针转Symbol</h2>
<h3 id="使用IQR方法进行重复值的选择">使用IQR方法进行重复值的选择</h3>
<p>使用 rownames(df) &lt;- rowNn 时经常会遇到rowNn中有重复值的情况，此时需要使用合适的策略来选择需要保留的那一列。下面这个函数默认保留IQR值(四分位距)最大的那一列。通过传入不同的select_func参数值，也可以改用其他的保留选择策略。如 mean 来保留算数平均值最大的一列，也可以传入自己定义的函数。</p>
<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><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br></pre></td><td class="code"><pre><code class="hljs R">f_rm_duplicated <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>NameL<span class="hljs-punctuation">,</span> reverse<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    tmp <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span>table<span class="hljs-punctuation">(</span>NameL<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>reverse<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        tmp <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-operator">$</span>NameL<span class="hljs-punctuation">[</span>tmp<span class="hljs-operator">$</span>Freq <span class="hljs-operator">&gt;</span> <span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>        tmp <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-operator">$</span>NameL<span class="hljs-punctuation">[</span>tmp<span class="hljs-operator">$</span>Freq <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-punctuation">&#125;</span><br>    which<span class="hljs-punctuation">(</span>NameL <span class="hljs-operator">%in%</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>f_dedup_IQR <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> rowNn<span class="hljs-punctuation">,</span> select_func<span class="hljs-operator">=</span><span class="hljs-string">&#x27;IQR&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>typeof<span class="hljs-punctuation">(</span>select_func<span class="hljs-punctuation">)</span> <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;character&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        select_func <span class="hljs-operator">=</span> get<span class="hljs-punctuation">(</span>select_func<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-comment"># 拆出无重复的数据，后续不进行处理</span><br>    noDup <span class="hljs-operator">&lt;-</span> f_rm_duplicated<span class="hljs-punctuation">(</span>rowNn<span class="hljs-punctuation">)</span><br>    tmp <span class="hljs-operator">&lt;-</span> rowNn<span class="hljs-punctuation">[</span>noDup<span class="hljs-punctuation">]</span><br>    noDup <span class="hljs-operator">&lt;-</span> df<span class="hljs-punctuation">[</span>noDup<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    rownames<span class="hljs-punctuation">(</span>noDup<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> tmp<br>    <span class="hljs-comment"># 拆除有重复的数据</span><br>    Dup <span class="hljs-operator">&lt;-</span> f_rm_duplicated<span class="hljs-punctuation">(</span>rowNn<span class="hljs-punctuation">,</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>    rowNn <span class="hljs-operator">&lt;-</span> rowNn<span class="hljs-punctuation">[</span>Dup<span class="hljs-punctuation">]</span><br>    Dup <span class="hljs-operator">&lt;-</span> df<span class="hljs-punctuation">[</span>Dup<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    rownames<span class="hljs-punctuation">(</span>Dup<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-literal">NULL</span><br>    <span class="hljs-comment"># 处理重复的数据</span><br>    lc_tmp <span class="hljs-operator">=</span> by<span class="hljs-punctuation">(</span>Dup<span class="hljs-punctuation">,</span><br>         rowNn<span class="hljs-punctuation">,</span><br>         <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>rownames<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>which.max<span class="hljs-punctuation">(</span>apply<span class="hljs-punctuation">(</span>X <span class="hljs-operator">=</span> x<span class="hljs-punctuation">,</span> FUN <span class="hljs-operator">=</span> select_func<span class="hljs-punctuation">,</span> MARGIN <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">)</span><br>    lc_probes <span class="hljs-operator">=</span> <span class="hljs-built_in">as.integer</span><span class="hljs-punctuation">(</span>lc_tmp<span class="hljs-punctuation">)</span><br>    Dup <span class="hljs-operator">=</span> Dup<span class="hljs-punctuation">[</span>lc_probes<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    rownames<span class="hljs-punctuation">(</span>Dup<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> rowNn<span class="hljs-punctuation">[</span>lc_probes<span class="hljs-punctuation">]</span><br>    <span class="hljs-comment"># 合并数据并返回</span><br>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>rbind<span class="hljs-punctuation">(</span>noDup<span class="hljs-punctuation">,</span>Dup<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
<h3 id="探针转Symbol-2">探针转Symbol</h3>
<ul>
<li>data.raw@annotation 可以得到注释的包信息，如pd.hg.u133a.2</li>
<li>在<a href="https://hexo.limour.top/go/#aHR0cHM6Ly93d3cuYmlvY29uZHVjdG9yLm9yZy8=" rel="noopener external nofollow noreferrer">bioconductor</a>上搜索pd.hg.u133a.2，可以知道其Platform为HG-U133A_2</li>
<li>谷歌搜索 HG-U133A_2 + affymetrix，可以找到affymetrix官网对应的页面</li>
<li>谷歌搜索 affymetrix “HG-U133A_2” site:www.ncbi.nlm.nih.gov，随便进一个GSE页面，找到对应的Platforms，如 GPL571 [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array，说明HG-U133A_2对应GPL571</li>
</ul>
<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><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br></pre></td><td class="code"><pre><code class="hljs R">require<span class="hljs-punctuation">(</span>GEOquery<span class="hljs-punctuation">)</span><br>f_getGPL <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_GPLN<span class="hljs-punctuation">,</span> lc_local <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    options<span class="hljs-punctuation">(</span>stringsAsFactors <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span><span class="hljs-operator">!</span>file.exists<span class="hljs-punctuation">(</span>lc_GPLN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>dir.create<span class="hljs-punctuation">(</span>lc_GPLN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>lc_local<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        gpl<span class="hljs-operator">=</span>read.table<span class="hljs-punctuation">(</span>file.path<span class="hljs-punctuation">(</span>lc_GPLN<span class="hljs-punctuation">,</span> lc_GPLN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>               header <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span>fill <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span>sep <span class="hljs-operator">=</span> <span class="hljs-string">&quot;\t&quot;</span><span class="hljs-punctuation">,</span><br>               comment.char <span class="hljs-operator">=</span> <span class="hljs-string">&quot;#&quot;</span><span class="hljs-punctuation">,</span><br>               stringsAsFactors <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span><br>               <span class="hljs-built_in">quote</span> <span class="hljs-operator">=</span> <span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">)</span><br>        <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>gpl<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>Table<span class="hljs-punctuation">(</span>getGEO<span class="hljs-punctuation">(</span>lc_GPLN<span class="hljs-punctuation">,</span>destdir <span class="hljs-operator">=</span> lc_GPLN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br><span class="hljs-punctuation">&#125;</span><br>GPL <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&#x27;GPL6244&#x27;</span><br>GPL <span class="hljs-operator">&lt;-</span> f_getGPL<span class="hljs-punctuation">(</span>GPL<span class="hljs-punctuation">)</span><br>GPL<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;Symbol&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> GPL<span class="hljs-operator">$</span>gene_assignment<br>GPL <span class="hljs-operator">&lt;-</span> GPL<span class="hljs-punctuation">[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;ID&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Symbol&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>GPL<span class="hljs-punctuation">[</span>GPL<span class="hljs-operator">$</span>Symbol <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;---&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Symbol&#x27;</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;---//---&#x27;</span><br>tmp <span class="hljs-operator">&lt;-</span> strsplit<span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span> GPL<span class="hljs-operator">$</span>Symbol<span class="hljs-punctuation">,</span> split <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;//&#x27;</span><span class="hljs-punctuation">)</span><br>tmp <span class="hljs-operator">&lt;-</span> lapply<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> FUN <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>x<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">)</span><br>GPL<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;Symbol&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> unlist<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><br>GPL<span class="hljs-operator">$</span>Symbol<span class="hljs-punctuation">[</span>GPL<span class="hljs-operator">$</span>Symbol <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;---&#x27;</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> GPL<span class="hljs-operator">$</span>ID<span class="hljs-punctuation">[</span>GPL<span class="hljs-operator">$</span>Symbol <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;---&#x27;</span><span class="hljs-punctuation">]</span><br>rownames<span class="hljs-punctuation">(</span>GPL<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>GPL<span class="hljs-operator">$</span>ID<span class="hljs-punctuation">)</span><br>GPL <span class="hljs-operator">&lt;-</span> GPL<span class="hljs-punctuation">[</span><span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>rownames<span class="hljs-punctuation">(</span>data.exprs<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>data.exprs <span class="hljs-operator">&lt;-</span> f_dedup_IQR<span class="hljs-punctuation">(</span>data.exprs<span class="hljs-punctuation">,</span> GPL<span class="hljs-operator">$</span>Symbol<span class="hljs-punctuation">)</span><br>data.exprs<br></code></pre></td></tr></table></figure>
<h2 id="GPL与Platform对应表">GPL与Platform对应表</h2>
<table>
<thead>
<tr>
<th>gpl</th>
<th>bioc_package</th>
<th>title</th>
</tr>
</thead>
<tbody>
<tr>
<td>GPL32</td>
<td>mgu74a</td>
<td>[MG_U74A] Affymetrix Murine Genome U74A Array</td>
</tr>
<tr>
<td>GPL33</td>
<td>mgu74b</td>
<td>[MG_U74B] Affymetrix Murine Genome U74B Array</td>
</tr>
<tr>
<td>GPL34</td>
<td>mgu74c</td>
<td>[MG_U74C] Affymetrix Murine Genome U74C Array</td>
</tr>
<tr>
<td>GPL71</td>
<td>ag</td>
<td>[AG] Affymetrix Arabidopsis Genome Array</td>
</tr>
<tr>
<td>GPL72</td>
<td>drosgenome1</td>
<td>[DrosGenome1] Affymetrix Drosophila Genome Array</td>
</tr>
<tr>
<td>GPL74</td>
<td>hcg110</td>
<td>[HC_G110] Affymetrix Human Cancer Array</td>
</tr>
<tr>
<td>GPL75</td>
<td>mu11ksuba</td>
<td>[Mu11KsubA] Affymetrix Murine 11K SubA Array</td>
</tr>
<tr>
<td>GPL76</td>
<td>mu11ksubb</td>
<td>[Mu11KsubB] Affymetrix Murine 11K SubB Array</td>
</tr>
<tr>
<td>GPL77</td>
<td>mu19ksuba</td>
<td>[Mu19KsubA] Affymetrix Murine 19K SubA Array</td>
</tr>
<tr>
<td>GPL78</td>
<td>mu19ksubb</td>
<td>[Mu19KsubB] Affymetrix Murine 19K SubB Array</td>
</tr>
<tr>
<td>GPL79</td>
<td>mu19ksubc</td>
<td>[Mu19KsubC] Affymetrix Murine 19K SubC Array</td>
</tr>
<tr>
<td>GPL80</td>
<td>hu6800</td>
<td>[Hu6800] Affymetrix Human Full Length HuGeneFL Array</td>
</tr>
<tr>
<td>GPL81</td>
<td>mgu74av2</td>
<td>[MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array</td>
</tr>
<tr>
<td>GPL82</td>
<td>mgu74bv2</td>
<td>[MG_U74Bv2] Affymetrix Murine Genome U74B Version 2 Array</td>
</tr>
<tr>
<td>GPL83</td>
<td>mgu74cv2</td>
<td>[MG_U74Cv2] Affymetrix Murine Genome U74 Version 2 Array</td>
</tr>
<tr>
<td>GPL85</td>
<td>rgu34a</td>
<td>[RG_U34A] Affymetrix Rat Genome U34 Array</td>
</tr>
<tr>
<td>GPL86</td>
<td>rgu34b</td>
<td>[RG_U34B] Affymetrix Rat Genome U34 Array</td>
</tr>
<tr>
<td>GPL87</td>
<td>rgu34c</td>
<td>[RG_U34C] Affymetrix Rat Genome U34 Array</td>
</tr>
<tr>
<td>GPL88</td>
<td>rnu34</td>
<td>[RN_U34] Affymetrix Rat Neurobiology U34 Array</td>
</tr>
<tr>
<td>GPL89</td>
<td>rtu34</td>
<td>[RT_U34] Affymetrix Rat Toxicology U34 Array</td>
</tr>
<tr>
<td>GPL90</td>
<td>ygs98</td>
<td>[YG_S98] Affymetrix Yeast Genome S98 Array</td>
</tr>
<tr>
<td>GPL91</td>
<td>hgu95av2</td>
<td>[HG_U95A] Affymetrix Human Genome U95A Array</td>
</tr>
<tr>
<td>GPL92</td>
<td>hgu95b</td>
<td>[HG_U95B] Affymetrix Human Genome U95B Array</td>
</tr>
<tr>
<td>GPL93</td>
<td>hgu95c</td>
<td>[HG_U95C] Affymetrix Human Genome U95C Array</td>
</tr>
<tr>
<td>GPL94</td>
<td>hgu95d</td>
<td>[HG_U95D] Affymetrix Human Genome U95D Array</td>
</tr>
<tr>
<td>GPL95</td>
<td>hgu95e</td>
<td>[HG_U95E] Affymetrix Human Genome U95E Array</td>
</tr>
<tr>
<td>GPL96</td>
<td>hgu133a</td>
<td>[HG-U133A] Affymetrix Human Genome U133A Array</td>
</tr>
<tr>
<td>GPL97</td>
<td>hgu133b</td>
<td>[HG-U133B] Affymetrix Human Genome U133B Array</td>
</tr>
<tr>
<td>GPL98</td>
<td>hu35ksuba</td>
<td>[Hu35KsubA] Affymetrix Human 35K SubA Array</td>
</tr>
<tr>
<td>GPL99</td>
<td>hu35ksubb</td>
<td>[Hu35KsubB] Affymetrix Human 35K SubB Array</td>
</tr>
<tr>
<td>GPL100</td>
<td>hu35ksubc</td>
<td>[Hu35KsubC] Affymetrix Human 35K SubC Array</td>
</tr>
<tr>
<td>GPL101</td>
<td>hu35ksubd</td>
<td>[Hu35KsubD] Affymetrix Human 35K SubD Array</td>
</tr>
<tr>
<td>GPL198</td>
<td>ath1121501</td>
<td>[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array</td>
</tr>
<tr>
<td>GPL199</td>
<td>ecoli2</td>
<td>[Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array</td>
</tr>
<tr>
<td>GPL200</td>
<td>celegans</td>
<td>[Celegans] Affymetrix C. elegans Genome Array</td>
</tr>
<tr>
<td>GPL201</td>
<td>hgfocus</td>
<td>[HG-Focus] Affymetrix Human HG-Focus Target Array</td>
</tr>
<tr>
<td>GPL339</td>
<td>moe430a</td>
<td>[MOE430A] Affymetrix Mouse Expression 430A Array</td>
</tr>
<tr>
<td>GPL340</td>
<td>mouse4302</td>
<td>[MOE430B] Affymetrix Mouse Expression 430B Array</td>
</tr>
<tr>
<td>GPL341</td>
<td>rae230a</td>
<td>[RAE230A] Affymetrix Rat Expression 230A Array</td>
</tr>
<tr>
<td>GPL342</td>
<td>rae230b</td>
<td>[RAE230B] Affymetrix Rat Expression 230B Array</td>
</tr>
<tr>
<td>GPL570</td>
<td>hgu133plus2</td>
<td>[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array</td>
</tr>
<tr>
<td>GPL571</td>
<td>hgu133a2</td>
<td>[HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array</td>
</tr>
<tr>
<td>GPL886</td>
<td>hgug4111a</td>
<td>Agilent-011871 Human 1B Microarray G4111A (Feature Number version)</td>
</tr>
<tr>
<td>GPL887</td>
<td>hgug4110b</td>
<td>Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version)</td>
</tr>
<tr>
<td>GPL1261</td>
<td>mouse430a2</td>
<td>[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array</td>
</tr>
<tr>
<td>GPL1318</td>
<td>xenopuslaevis</td>
<td>[Xenopus_laevis] Affymetrix Xenopus laevis Genome Array</td>
</tr>
<tr>
<td>GPL1319</td>
<td>zebrafish</td>
<td>[Zebrafish] Affymetrix Zebrafish Genome Array</td>
</tr>
<tr>
<td>GPL1322</td>
<td>drosophila2</td>
<td>[Drosophila_2] Affymetrix Drosophila Genome 2.0 Array</td>
</tr>
<tr>
<td>GPL1352</td>
<td>u133x3p</td>
<td>[U133_X3P] Affymetrix Human X3P Array</td>
</tr>
<tr>
<td>GPL1355</td>
<td>rat2302</td>
<td>[Rat230_2] Affymetrix Rat Genome 230 2.0 Array</td>
</tr>
<tr>
<td>GPL1708</td>
<td>hgug4112a</td>
<td>Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version)</td>
</tr>
<tr>
<td>GPL2112</td>
<td>bovine</td>
<td>[Bovine] Affymetrix Bovine Genome Array</td>
</tr>
<tr>
<td>GPL2529</td>
<td>yeast2</td>
<td>[Yeast_2] Affymetrix Yeast Genome 2.0 Array</td>
</tr>
<tr>
<td>GPL2891</td>
<td>h20kcod</td>
<td>GE Healthcare/Amersham Biosciences CodeLink™ UniSet Human 20K I Bioarray</td>
</tr>
<tr>
<td>GPL2898</td>
<td>adme16cod</td>
<td>GE Healthcare/Amersham Biosciences CodeLink™ ADME Rat 16-Assay Bioarray</td>
</tr>
<tr>
<td>GPL3154</td>
<td>ecoli2</td>
<td>[E_coli_2] Affymetrix E. coli Genome 2.0 Array</td>
</tr>
<tr>
<td>GPL3213</td>
<td>chicken</td>
<td>[Chicken] Affymetrix Chicken Genome Array</td>
</tr>
<tr>
<td>GPL3533</td>
<td>porcine</td>
<td>[Porcine] Affymetrix Porcine Genome Array</td>
</tr>
<tr>
<td>GPL3738</td>
<td>canine2</td>
<td>[Canine_2] Affymetrix Canine Genome 2.0 Array</td>
</tr>
<tr>
<td>GPL3921</td>
<td>hthgu133a</td>
<td>[HT_HG-U133A] Affymetrix HT Human Genome U133A Array</td>
</tr>
<tr>
<td>GPL3979</td>
<td>canine</td>
<td>[Canine] Affymetrix Canine Genome 1.0 Array</td>
</tr>
<tr>
<td>GPL4032</td>
<td></td>
<td>[Maize] Affymetrix Maize Genome Array</td>
</tr>
<tr>
<td>GPL4191</td>
<td>h10kcod</td>
<td>CodeLink UniSet Human I Bioarray</td>
</tr>
<tr>
<td>GPL5188</td>
<td>huex10sttranscriptcluster</td>
<td>[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version]</td>
</tr>
<tr>
<td>GPL5689</td>
<td>hgug4100a</td>
<td>Agilent Human 1 cDNA Microarray (G4100A) [layout C]</td>
</tr>
<tr>
<td>GPL6097</td>
<td>illuminaHumanv1</td>
<td>Illumina human-6 v1.0 expression beadchip</td>
</tr>
<tr>
<td>GPL6102</td>
<td>illuminaHumanv2</td>
<td>Illumina human-6 v2.0 expression beadchip</td>
</tr>
<tr>
<td>GPL6244</td>
<td>hugene10sttranscriptcluster</td>
<td>[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]</td>
</tr>
<tr>
<td>GPL6246</td>
<td>mogene10sttranscriptcluster</td>
<td>[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]</td>
</tr>
<tr>
<td>GPL6885</td>
<td>illuminaMousev2</td>
<td>Illumina MouseRef-8 v2.0 expression beadchip</td>
</tr>
<tr>
<td>GPL6947</td>
<td>illuminaHumanv3</td>
<td>Illumina HumanHT-12 V3.0 expression beadchip</td>
</tr>
<tr>
<td>GPL8300</td>
<td>hgu95av2</td>
<td>[HG_U95Av2] Affymetrix Human Genome U95 Version 2 Array</td>
</tr>
<tr>
<td>GPL8321</td>
<td>mouse430a2</td>
<td>[Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 Array</td>
</tr>
<tr>
<td>GPL8490</td>
<td>IlluminaHumanMethylation27k</td>
<td>Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)</td>
</tr>
<tr>
<td>GPL10558</td>
<td>illuminaHumanv4</td>
<td>Illumina HumanHT-12 V4.0 expression beadchip</td>
</tr>
<tr>
<td>GPL11532</td>
<td>hugene11sttranscriptcluster</td>
<td>[HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [transcript (gene) version]</td>
</tr>
<tr>
<td>GPL13497</td>
<td>HsAgilentDesign026652</td>
<td>Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Probe Name version)</td>
</tr>
<tr>
<td>GPL13534</td>
<td>IlluminaHumanMethylation450k</td>
<td>Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)</td>
</tr>
<tr>
<td>GPL13667</td>
<td>hgu219</td>
<td>[HG-U219] Affymetrix Human Genome U219 Array</td>
</tr>
<tr>
<td>GPL14877</td>
<td>hgu133plus2</td>
<td>Affymetrix Human Genome U133 Plus 2.0 Array [Brainarray Version 13, HGU133Plus2_Hs_ENTREZG]</td>
</tr>
<tr>
<td>GPL15380</td>
<td>GGHumanMethCancerPanelv1</td>
<td>Illumina Sentrix Array Matrix (SAM) - GoldenGate Methylation Cancer Panel I</td>
</tr>
<tr>
<td>GPL15396</td>
<td>hthgu133b</td>
<td>[HT_HG-U133B] Affymetrix HT Human Genome U133B Array [custom CDF: ENTREZ brainarray v. 14]</td>
</tr>
<tr>
<td>GPL17556</td>
<td>hugene10sttranscriptcluster</td>
<td>[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZG_17.0.0]</td>
</tr>
<tr>
<td>GPL17897</td>
<td>hthgu133a</td>
<td>[HT_HG-U133A] Affymetrix Human Genome U133A Array (custom CDF: HTHGU133A_Hs_ENTREZG.cdf version 17.0.0)</td>
</tr>
<tr>
<td>GPL18190</td>
<td>hugene11sttranscriptcluster</td>
<td>[HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [CDF: Brainarray HuGene11stv1_Hs_ENTREZG_15.1.0]</td>
</tr>
</tbody>
</table>

                
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    Fluid.events.registerRefreshCallback(function() {
      if ('anchors' in window) {
        anchors.removeAll();
        var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
        var res = [];
        for (var item of el) {
          res.push('.markdown-body > ' + item.trim());
        }
        if (CONFIG.anchorjs.placement === 'left') {
          anchors.options.class = 'anchorjs-link-left';
        }
        anchors.add(res.join(', '));
      }
    });
  });
</script>


  <script>Fluid.plugins.imageCaption();</script>

  <script  src="/js/local-search.js" ></script>


<!-- 主题的启动项，将它保持在最底部 -->
<!-- the boot of the theme, keep it at the bottom -->
<script  src="/js/boot.js" ></script>


  <noscript>
    <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  </noscript>
<!-- hexo injector body_end start -->
  <script defer src="/theme-inject/timeliness.js"></script>
<!-- hexo injector body_end end --></body>
</html>