oligo-GEO-ArrayExpress-xin-pian-shu-ju-chu-li.html 58 KB

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  166. <h1 id="seo-header">【迁移】oligo:GEO/ArrayExpress芯片数据处理</h1>
  167. <p id="updated-time" class="note note-info" style="">
  168. Last updated on March 19, 2024 pm
  169. </p>
  170. <div class="markdown-body">
  171. <h2 id="安装依赖">安装依赖</h2>
  172. <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><span class="line">conda clean -y -all</span><br><span class="line">conda create -n geo -c conda-forge r-base=4.1.3</span><br><span class="line">conda activate geo</span><br><span class="line">conda install -c conda-forge r-tidyverse=1.3.1 -y</span><br><span class="line">conda install -c conda-forge r-irkernel -y</span><br><span class="line">conda install -c conda-forge r-r.utils -y</span><br><span class="line">conda install -c conda-forge r-rcolorbrewer -y</span><br><span class="line">Rscript -e <span class="string">&quot;IRkernel::installspec(name=&#x27;geo&#x27;, displayname=&#x27;r-geo&#x27;)&quot;</span></span><br><span class="line">conda install -c bioconda bioconductor-geoquery -y</span><br><span class="line">conda install -c bioconda bioconductor-oligo -y</span><br><span class="line">conda install -c bioconda bioconductor-affy -y</span><br><span class="line">conda install -c bioconda bioconductor-pd.hugene.1.0.st.v1 -y <span class="comment"># read.celfiles 需要啥安装啥</span></span><br><span class="line">conda install -c bioconda bioconductor-pd.hg.u133a.2 -y</span><br><span class="line">conda install -c bioconda bioconductor-arrayexpress -y</span><br><span class="line">conda install -c bioconda bioconductor-biomart -y</span><br><span class="line">conda install -c bioconda bioconductor-affycoretools -y</span><br></pre></td></tr></table></figure>
  173. <h2 id="下载芯片数据">下载芯片数据</h2>
  174. <h3 id="GEO">GEO</h3>
  175. <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><span class="line">library<span class="punctuation">(</span>GEOquery<span class="punctuation">)</span></span><br><span class="line">library<span class="punctuation">(</span>oligo<span class="punctuation">)</span></span><br><span class="line">library<span class="punctuation">(</span>affy<span class="punctuation">)</span></span><br><span class="line">gse<span class="operator">=</span><span class="string">&quot;GSE43332&quot;</span></span><br><span class="line">rawdata <span class="operator">&lt;-</span> getGEOSuppFiles<span class="punctuation">(</span>gse<span class="punctuation">)</span> <span class="comment">#下载原始数据</span></span><br><span class="line">rawdata</span><br><span class="line">setwd<span class="punctuation">(</span>gse<span class="punctuation">)</span></span><br><span class="line">untar<span class="punctuation">(</span><span class="string">&quot;GSE43332_RAW.tar&quot;</span><span class="punctuation">,</span>exdir <span class="operator">=</span> <span class="string">&quot;.&quot;</span><span class="punctuation">)</span></span><br><span class="line">celfiles <span class="operator">&lt;-</span> list.files<span class="punctuation">(</span>pattern <span class="operator">=</span> <span class="string">&quot;*CEL.gz$&quot;</span><span class="punctuation">)</span> <span class="comment">#批量查找并列出后缀为.gz的文件</span></span><br><span class="line">data.raw <span class="operator">&lt;-</span> read.celfiles<span class="punctuation">(</span>celfiles<span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
  176. <h3 id="ArrayExpress">ArrayExpress</h3>
  177. <ul>
  178. <li>~/dev/xray/xray -c ~/etc/xui2.json &amp;</li>
  179. <li>wget -e “https_proxy=<a target="_blank" rel="noopener" href="http://127.0.0.1:20809">http://127.0.0.1:20809</a>” <a target="_blank" rel="noopener" href="https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-1422/E-MEXP-1422.raw.1.zip">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>
  180. <li>unzip E-MEXP-1422.raw.1.zip</li>
  181. </ul>
  182. <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><span class="line">library<span class="punctuation">(</span>ArrayExpress<span class="punctuation">)</span></span><br><span class="line">library<span class="punctuation">(</span>oligo<span class="punctuation">)</span></span><br><span class="line">library<span class="punctuation">(</span>affy<span class="punctuation">)</span></span><br><span class="line"><span class="comment"># Sys.setenv(&quot;http_proxy&quot;=&quot;http://127.0.0.1:20809&quot;)</span></span><br><span class="line"><span class="comment"># Sys.setenv(&quot;https_proxy&quot;=&quot;http://127.0.0.1:20809&quot;)</span></span><br><span class="line"><span class="comment"># mexp1422=getAE(&quot;E-MTAB-6128&quot;, type = &#x27;raw&#x27;, extract = T)</span></span><br><span class="line">celfiles <span class="operator">&lt;-</span> list.files<span class="punctuation">(</span>pattern <span class="operator">=</span> <span class="string">&quot;*.CEL$&quot;</span><span class="punctuation">)</span> <span class="comment">#批量查找并列出后缀为CEL的文件</span></span><br><span class="line">data.raw <span class="operator">&lt;-</span> read.celfiles<span class="punctuation">(</span>celfiles<span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
  183. <h2 id="RMA标准化数据">RMA标准化数据</h2>
  184. <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><span class="line">sampleNames<span class="punctuation">(</span>data.raw<span class="punctuation">)</span> <span class="operator">&lt;-</span> sapply<span class="punctuation">(</span>strsplit<span class="punctuation">(</span>sampleNames<span class="punctuation">(</span>data.raw<span class="punctuation">)</span><span class="punctuation">,</span><span class="string">&quot;_&quot;</span><span class="punctuation">,</span>fixed<span class="operator">=</span><span class="built_in">T</span><span class="punctuation">)</span><span class="punctuation">,</span> <span class="string">&quot;[&quot;</span><span class="punctuation">,</span><span class="number">1</span><span class="punctuation">)</span></span><br><span class="line">sampleNames<span class="punctuation">(</span>data.raw<span class="punctuation">)</span></span><br><span class="line"> </span><br><span class="line">fit1 <span class="operator">&lt;-</span> fitProbeLevelModel<span class="punctuation">(</span>data.raw<span class="punctuation">)</span></span><br><span class="line"> </span><br><span class="line">image<span class="punctuation">(</span>fit1<span class="punctuation">,</span>type<span class="operator">=</span><span class="string">&quot;weights&quot;</span><span class="punctuation">,</span>which<span class="operator">=</span><span class="number">1</span><span class="punctuation">,</span>main<span class="operator">=</span><span class="string">&quot;weights&quot;</span><span class="punctuation">)</span></span><br><span class="line">image<span class="punctuation">(</span>fit1<span class="punctuation">,</span>type<span class="operator">=</span><span class="string">&quot;residuals&quot;</span><span class="punctuation">,</span>which<span class="operator">=</span><span class="number">1</span><span class="punctuation">,</span>main<span class="operator">=</span><span class="string">&quot;Residuals&quot;</span><span class="punctuation">)</span></span><br><span class="line">image<span class="punctuation">(</span>fit1<span class="punctuation">,</span>type<span class="operator">=</span><span class="string">&quot;sign.residuals&quot;</span><span class="punctuation">,</span>which<span class="operator">=</span><span class="number">1</span><span class="punctuation">,</span>main<span class="operator">=</span><span class="string">&quot;Residuals.sign&quot;</span><span class="punctuation">)</span></span><br><span class="line"> </span><br><span class="line">data.eset <span class="operator">&lt;-</span> oligo<span class="operator">::</span>rma<span class="punctuation">(</span>data.raw<span class="punctuation">)</span></span><br><span class="line">data.exprs <span class="operator">&lt;-</span> exprs<span class="punctuation">(</span>data.eset<span class="punctuation">)</span></span><br><span class="line"> </span><br><span class="line">library<span class="punctuation">(</span>RColorBrewer<span class="punctuation">)</span></span><br><span class="line">display.brewer.all<span class="punctuation">(</span><span class="punctuation">)</span></span><br><span class="line"><span class="keyword">if</span><span class="punctuation">(</span>ncol<span class="punctuation">(</span>data.eset<span class="punctuation">)</span><span class="operator">&gt;</span><span class="number">8</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line"> colors <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span>brewer.pal<span class="punctuation">(</span><span class="number">8</span><span class="punctuation">,</span><span class="string">&quot;Set2&quot;</span><span class="punctuation">)</span><span class="punctuation">,</span>brewer.pal<span class="punctuation">(</span>ncol<span class="punctuation">(</span>data.eset<span class="punctuation">)</span><span class="operator">-</span><span class="number">8</span><span class="punctuation">,</span><span class="string">&quot;Set1&quot;</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span><span class="keyword">else</span><span class="punctuation">&#123;</span></span><br><span class="line"> colors <span class="operator">&lt;-</span> brewer.pal<span class="punctuation">(</span>ncol<span class="punctuation">(</span>data.eset<span class="punctuation">)</span><span class="punctuation">,</span><span class="string">&quot;Set2&quot;</span><span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">boxplot<span class="punctuation">(</span>data.exprs<span class="punctuation">,</span>col<span class="operator">=</span>colors<span class="punctuation">,</span>main<span class="operator">=</span><span class="string">&quot;afterRMA&quot;</span><span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
  185. <h2 id="探针转Symbol">探针转Symbol</h2>
  186. <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>
  187. <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>
  188. <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><span class="line">f_rm_duplicated <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>NameL<span class="punctuation">,</span> reverse<span class="operator">=</span><span class="built_in">F</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line"> tmp <span class="operator">&lt;-</span> data.frame<span class="punctuation">(</span>table<span class="punctuation">(</span>NameL<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"> <span class="keyword">if</span><span class="punctuation">(</span>reverse<span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line"> tmp <span class="operator">&lt;-</span> tmp<span class="operator">$</span>NameL<span class="punctuation">[</span>tmp<span class="operator">$</span>Freq <span class="operator">&gt;</span> <span class="number">1</span><span class="punctuation">]</span></span><br><span class="line"> <span class="punctuation">&#125;</span><span class="keyword">else</span><span class="punctuation">&#123;</span></span><br><span class="line"> tmp <span class="operator">&lt;-</span> tmp<span class="operator">$</span>NameL<span class="punctuation">[</span>tmp<span class="operator">$</span>Freq <span class="operator">==</span> <span class="number">1</span><span class="punctuation">]</span></span><br><span class="line"> <span class="punctuation">&#125;</span></span><br><span class="line"> which<span class="punctuation">(</span>NameL <span class="operator">%in%</span> <span class="built_in">as.character</span><span class="punctuation">(</span>tmp<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">f_dedup_IQR <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>df<span class="punctuation">,</span> rowNn<span class="punctuation">,</span> select_func<span class="operator">=</span><span class="string">&#x27;IQR&#x27;</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line"> <span class="keyword">if</span><span class="punctuation">(</span>typeof<span class="punctuation">(</span>select_func<span class="punctuation">)</span> <span class="operator">==</span> <span class="string">&#x27;character&#x27;</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line"> select_func <span class="operator">=</span> get<span class="punctuation">(</span>select_func<span class="punctuation">)</span></span><br><span class="line"> <span class="punctuation">&#125;</span></span><br><span class="line"> <span class="comment"># 拆出无重复的数据,后续不进行处理</span></span><br><span class="line"> noDup <span class="operator">&lt;-</span> f_rm_duplicated<span class="punctuation">(</span>rowNn<span class="punctuation">)</span></span><br><span class="line"> tmp <span class="operator">&lt;-</span> rowNn<span class="punctuation">[</span>noDup<span class="punctuation">]</span></span><br><span class="line"> noDup <span class="operator">&lt;-</span> df<span class="punctuation">[</span>noDup<span class="punctuation">,</span><span class="punctuation">]</span></span><br><span class="line"> rownames<span class="punctuation">(</span>noDup<span class="punctuation">)</span> <span class="operator">&lt;-</span> tmp</span><br><span class="line"> <span class="comment"># 拆除有重复的数据</span></span><br><span class="line"> Dup <span class="operator">&lt;-</span> f_rm_duplicated<span class="punctuation">(</span>rowNn<span class="punctuation">,</span> <span class="built_in">T</span><span class="punctuation">)</span></span><br><span class="line"> rowNn <span class="operator">&lt;-</span> rowNn<span class="punctuation">[</span>Dup<span class="punctuation">]</span></span><br><span class="line"> Dup <span class="operator">&lt;-</span> df<span class="punctuation">[</span>Dup<span class="punctuation">,</span><span class="punctuation">]</span></span><br><span class="line"> rownames<span class="punctuation">(</span>Dup<span class="punctuation">)</span> <span class="operator">&lt;-</span> <span class="literal">NULL</span></span><br><span class="line"> <span class="comment"># 处理重复的数据</span></span><br><span class="line"> lc_tmp <span class="operator">=</span> by<span class="punctuation">(</span>Dup<span class="punctuation">,</span></span><br><span class="line"> rowNn<span class="punctuation">,</span></span><br><span class="line"> <span class="keyword">function</span><span class="punctuation">(</span>x<span class="punctuation">)</span><span class="punctuation">&#123;</span>rownames<span class="punctuation">(</span>x<span class="punctuation">)</span><span class="punctuation">[</span>which.max<span class="punctuation">(</span>apply<span class="punctuation">(</span>X <span class="operator">=</span> x<span class="punctuation">,</span> FUN <span class="operator">=</span> select_func<span class="punctuation">,</span> MARGIN <span class="operator">=</span> <span class="number">1</span><span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">]</span><span class="punctuation">&#125;</span><span class="punctuation">)</span></span><br><span class="line"> lc_probes <span class="operator">=</span> <span class="built_in">as.integer</span><span class="punctuation">(</span>lc_tmp<span class="punctuation">)</span></span><br><span class="line"> Dup <span class="operator">=</span> Dup<span class="punctuation">[</span>lc_probes<span class="punctuation">,</span><span class="punctuation">]</span></span><br><span class="line"> rownames<span class="punctuation">(</span>Dup<span class="punctuation">)</span> <span class="operator">&lt;-</span> rowNn<span class="punctuation">[</span>lc_probes<span class="punctuation">]</span></span><br><span class="line"> <span class="comment"># 合并数据并返回</span></span><br><span class="line"> <span class="built_in">return</span><span class="punctuation">(</span>rbind<span class="punctuation">(</span>noDup<span class="punctuation">,</span>Dup<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br></pre></td></tr></table></figure>
  189. <h3 id="探针转Symbol-2">探针转Symbol</h3>
  190. <ul>
  191. <li>data.raw@annotation 可以得到注释的包信息,如pd.hg.u133a.2</li>
  192. <li>在<a target="_blank" rel="noopener" href="https://www.bioconductor.org/">bioconductor</a>上搜索pd.hg.u133a.2,可以知道其Platform为HG-U133A_2</li>
  193. <li>谷歌搜索 HG-U133A_2 + affymetrix,可以找到affymetrix官网对应的页面</li>
  194. <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>
  195. </ul>
  196. <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><span class="line">require<span class="punctuation">(</span>GEOquery<span class="punctuation">)</span></span><br><span class="line">f_getGPL <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>lc_GPLN<span class="punctuation">,</span> lc_local <span class="operator">=</span> <span class="built_in">F</span><span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line"> options<span class="punctuation">(</span>stringsAsFactors <span class="operator">=</span> <span class="built_in">F</span><span class="punctuation">)</span></span><br><span class="line"> <span class="keyword">if</span> <span class="punctuation">(</span><span class="operator">!</span>file.exists<span class="punctuation">(</span>lc_GPLN<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">&#123;</span>dir.create<span class="punctuation">(</span>lc_GPLN<span class="punctuation">)</span><span class="punctuation">&#125;</span></span><br><span class="line"> <span class="keyword">if</span><span class="punctuation">(</span>lc_local<span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line"> gpl<span class="operator">=</span>read.table<span class="punctuation">(</span>file.path<span class="punctuation">(</span>lc_GPLN<span class="punctuation">,</span> lc_GPLN<span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line"> header <span class="operator">=</span> <span class="literal">TRUE</span><span class="punctuation">,</span>fill <span class="operator">=</span> <span class="built_in">T</span><span class="punctuation">,</span>sep <span class="operator">=</span> <span class="string">&quot;\t&quot;</span><span class="punctuation">,</span></span><br><span class="line"> comment.char <span class="operator">=</span> <span class="string">&quot;#&quot;</span><span class="punctuation">,</span></span><br><span class="line"> stringsAsFactors <span class="operator">=</span> <span class="literal">FALSE</span><span class="punctuation">,</span></span><br><span class="line"> <span class="built_in">quote</span> <span class="operator">=</span> <span class="string">&quot;&quot;</span><span class="punctuation">)</span></span><br><span class="line"> <span class="built_in">return</span><span class="punctuation">(</span>gpl<span class="punctuation">)</span></span><br><span class="line"> <span class="punctuation">&#125;</span><span class="keyword">else</span><span class="punctuation">&#123;</span></span><br><span class="line"> <span class="built_in">return</span><span class="punctuation">(</span>Table<span class="punctuation">(</span>getGEO<span class="punctuation">(</span>lc_GPLN<span class="punctuation">,</span>destdir <span class="operator">=</span> lc_GPLN<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"> <span class="punctuation">&#125;</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line">GPL <span class="operator">&lt;-</span> <span class="string">&#x27;GPL6244&#x27;</span></span><br><span class="line">GPL <span class="operator">&lt;-</span> f_getGPL<span class="punctuation">(</span>GPL<span class="punctuation">)</span></span><br><span class="line">GPL<span class="punctuation">[[</span><span class="string">&#x27;Symbol&#x27;</span><span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">&lt;-</span> GPL<span class="operator">$</span>gene_assignment</span><br><span class="line">GPL <span class="operator">&lt;-</span> GPL<span class="punctuation">[</span><span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;ID&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;Symbol&#x27;</span><span class="punctuation">)</span><span class="punctuation">]</span></span><br><span class="line">GPL<span class="punctuation">[</span>GPL<span class="operator">$</span>Symbol <span class="operator">==</span> <span class="string">&#x27;---&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;Symbol&#x27;</span><span class="punctuation">]</span> <span class="operator">=</span> <span class="string">&#x27;---//---&#x27;</span></span><br><span class="line">tmp <span class="operator">&lt;-</span> strsplit<span class="punctuation">(</span>x <span class="operator">=</span> GPL<span class="operator">$</span>Symbol<span class="punctuation">,</span> split <span class="operator">=</span> <span class="string">&#x27;//&#x27;</span><span class="punctuation">)</span></span><br><span class="line">tmp <span class="operator">&lt;-</span> lapply<span class="punctuation">(</span>tmp<span class="punctuation">,</span> FUN <span class="operator">=</span> <span class="keyword">function</span><span class="punctuation">(</span>x<span class="punctuation">)</span><span class="punctuation">&#123;</span>x<span class="punctuation">[</span><span class="number">2</span><span class="punctuation">]</span><span class="punctuation">&#125;</span><span class="punctuation">)</span></span><br><span class="line">GPL<span class="punctuation">[[</span><span class="string">&#x27;Symbol&#x27;</span><span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">=</span> unlist<span class="punctuation">(</span>tmp<span class="punctuation">)</span></span><br><span class="line">GPL<span class="operator">$</span>Symbol<span class="punctuation">[</span>GPL<span class="operator">$</span>Symbol <span class="operator">==</span> <span class="string">&#x27;---&#x27;</span><span class="punctuation">]</span> <span class="operator">=</span> GPL<span class="operator">$</span>ID<span class="punctuation">[</span>GPL<span class="operator">$</span>Symbol <span class="operator">==</span> <span class="string">&#x27;---&#x27;</span><span class="punctuation">]</span></span><br><span class="line">rownames<span class="punctuation">(</span>GPL<span class="punctuation">)</span> <span class="operator">&lt;-</span> <span class="built_in">as.character</span><span class="punctuation">(</span>GPL<span class="operator">$</span>ID<span class="punctuation">)</span></span><br><span class="line">GPL <span class="operator">&lt;-</span> GPL<span class="punctuation">[</span><span class="built_in">as.character</span><span class="punctuation">(</span>rownames<span class="punctuation">(</span>data.exprs<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">,</span><span class="punctuation">]</span></span><br><span class="line">data.exprs <span class="operator">&lt;-</span> f_dedup_IQR<span class="punctuation">(</span>data.exprs<span class="punctuation">,</span> GPL<span class="operator">$</span>Symbol<span class="punctuation">)</span></span><br><span class="line">data.exprs</span><br></pre></td></tr></table></figure>
  197. <h2 id="GPL与Platform对应表">GPL与Platform对应表</h2>
  198. <table>
  199. <thead>
  200. <tr>
  201. <th>gpl</th>
  202. <th>bioc_package</th>
  203. <th>title</th>
  204. </tr>
  205. </thead>
  206. <tbody>
  207. <tr>
  208. <td>GPL32</td>
  209. <td>mgu74a</td>
  210. <td>[MG_U74A] Affymetrix Murine Genome U74A Array</td>
  211. </tr>
  212. <tr>
  213. <td>GPL33</td>
  214. <td>mgu74b</td>
  215. <td>[MG_U74B] Affymetrix Murine Genome U74B Array</td>
  216. </tr>
  217. <tr>
  218. <td>GPL34</td>
  219. <td>mgu74c</td>
  220. <td>[MG_U74C] Affymetrix Murine Genome U74C Array</td>
  221. </tr>
  222. <tr>
  223. <td>GPL71</td>
  224. <td>ag</td>
  225. <td>[AG] Affymetrix Arabidopsis Genome Array</td>
  226. </tr>
  227. <tr>
  228. <td>GPL72</td>
  229. <td>drosgenome1</td>
  230. <td>[DrosGenome1] Affymetrix Drosophila Genome Array</td>
  231. </tr>
  232. <tr>
  233. <td>GPL74</td>
  234. <td>hcg110</td>
  235. <td>[HC_G110] Affymetrix Human Cancer Array</td>
  236. </tr>
  237. <tr>
  238. <td>GPL75</td>
  239. <td>mu11ksuba</td>
  240. <td>[Mu11KsubA] Affymetrix Murine 11K SubA Array</td>
  241. </tr>
  242. <tr>
  243. <td>GPL76</td>
  244. <td>mu11ksubb</td>
  245. <td>[Mu11KsubB] Affymetrix Murine 11K SubB Array</td>
  246. </tr>
  247. <tr>
  248. <td>GPL77</td>
  249. <td>mu19ksuba</td>
  250. <td>[Mu19KsubA] Affymetrix Murine 19K SubA Array</td>
  251. </tr>
  252. <tr>
  253. <td>GPL78</td>
  254. <td>mu19ksubb</td>
  255. <td>[Mu19KsubB] Affymetrix Murine 19K SubB Array</td>
  256. </tr>
  257. <tr>
  258. <td>GPL79</td>
  259. <td>mu19ksubc</td>
  260. <td>[Mu19KsubC] Affymetrix Murine 19K SubC Array</td>
  261. </tr>
  262. <tr>
  263. <td>GPL80</td>
  264. <td>hu6800</td>
  265. <td>[Hu6800] Affymetrix Human Full Length HuGeneFL Array</td>
  266. </tr>
  267. <tr>
  268. <td>GPL81</td>
  269. <td>mgu74av2</td>
  270. <td>[MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array</td>
  271. </tr>
  272. <tr>
  273. <td>GPL82</td>
  274. <td>mgu74bv2</td>
  275. <td>[MG_U74Bv2] Affymetrix Murine Genome U74B Version 2 Array</td>
  276. </tr>
  277. <tr>
  278. <td>GPL83</td>
  279. <td>mgu74cv2</td>
  280. <td>[MG_U74Cv2] Affymetrix Murine Genome U74 Version 2 Array</td>
  281. </tr>
  282. <tr>
  283. <td>GPL85</td>
  284. <td>rgu34a</td>
  285. <td>[RG_U34A] Affymetrix Rat Genome U34 Array</td>
  286. </tr>
  287. <tr>
  288. <td>GPL86</td>
  289. <td>rgu34b</td>
  290. <td>[RG_U34B] Affymetrix Rat Genome U34 Array</td>
  291. </tr>
  292. <tr>
  293. <td>GPL87</td>
  294. <td>rgu34c</td>
  295. <td>[RG_U34C] Affymetrix Rat Genome U34 Array</td>
  296. </tr>
  297. <tr>
  298. <td>GPL88</td>
  299. <td>rnu34</td>
  300. <td>[RN_U34] Affymetrix Rat Neurobiology U34 Array</td>
  301. </tr>
  302. <tr>
  303. <td>GPL89</td>
  304. <td>rtu34</td>
  305. <td>[RT_U34] Affymetrix Rat Toxicology U34 Array</td>
  306. </tr>
  307. <tr>
  308. <td>GPL90</td>
  309. <td>ygs98</td>
  310. <td>[YG_S98] Affymetrix Yeast Genome S98 Array</td>
  311. </tr>
  312. <tr>
  313. <td>GPL91</td>
  314. <td>hgu95av2</td>
  315. <td>[HG_U95A] Affymetrix Human Genome U95A Array</td>
  316. </tr>
  317. <tr>
  318. <td>GPL92</td>
  319. <td>hgu95b</td>
  320. <td>[HG_U95B] Affymetrix Human Genome U95B Array</td>
  321. </tr>
  322. <tr>
  323. <td>GPL93</td>
  324. <td>hgu95c</td>
  325. <td>[HG_U95C] Affymetrix Human Genome U95C Array</td>
  326. </tr>
  327. <tr>
  328. <td>GPL94</td>
  329. <td>hgu95d</td>
  330. <td>[HG_U95D] Affymetrix Human Genome U95D Array</td>
  331. </tr>
  332. <tr>
  333. <td>GPL95</td>
  334. <td>hgu95e</td>
  335. <td>[HG_U95E] Affymetrix Human Genome U95E Array</td>
  336. </tr>
  337. <tr>
  338. <td>GPL96</td>
  339. <td>hgu133a</td>
  340. <td>[HG-U133A] Affymetrix Human Genome U133A Array</td>
  341. </tr>
  342. <tr>
  343. <td>GPL97</td>
  344. <td>hgu133b</td>
  345. <td>[HG-U133B] Affymetrix Human Genome U133B Array</td>
  346. </tr>
  347. <tr>
  348. <td>GPL98</td>
  349. <td>hu35ksuba</td>
  350. <td>[Hu35KsubA] Affymetrix Human 35K SubA Array</td>
  351. </tr>
  352. <tr>
  353. <td>GPL99</td>
  354. <td>hu35ksubb</td>
  355. <td>[Hu35KsubB] Affymetrix Human 35K SubB Array</td>
  356. </tr>
  357. <tr>
  358. <td>GPL100</td>
  359. <td>hu35ksubc</td>
  360. <td>[Hu35KsubC] Affymetrix Human 35K SubC Array</td>
  361. </tr>
  362. <tr>
  363. <td>GPL101</td>
  364. <td>hu35ksubd</td>
  365. <td>[Hu35KsubD] Affymetrix Human 35K SubD Array</td>
  366. </tr>
  367. <tr>
  368. <td>GPL198</td>
  369. <td>ath1121501</td>
  370. <td>[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array</td>
  371. </tr>
  372. <tr>
  373. <td>GPL199</td>
  374. <td>ecoli2</td>
  375. <td>[Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array</td>
  376. </tr>
  377. <tr>
  378. <td>GPL200</td>
  379. <td>celegans</td>
  380. <td>[Celegans] Affymetrix C. elegans Genome Array</td>
  381. </tr>
  382. <tr>
  383. <td>GPL201</td>
  384. <td>hgfocus</td>
  385. <td>[HG-Focus] Affymetrix Human HG-Focus Target Array</td>
  386. </tr>
  387. <tr>
  388. <td>GPL339</td>
  389. <td>moe430a</td>
  390. <td>[MOE430A] Affymetrix Mouse Expression 430A Array</td>
  391. </tr>
  392. <tr>
  393. <td>GPL340</td>
  394. <td>mouse4302</td>
  395. <td>[MOE430B] Affymetrix Mouse Expression 430B Array</td>
  396. </tr>
  397. <tr>
  398. <td>GPL341</td>
  399. <td>rae230a</td>
  400. <td>[RAE230A] Affymetrix Rat Expression 230A Array</td>
  401. </tr>
  402. <tr>
  403. <td>GPL342</td>
  404. <td>rae230b</td>
  405. <td>[RAE230B] Affymetrix Rat Expression 230B Array</td>
  406. </tr>
  407. <tr>
  408. <td>GPL570</td>
  409. <td>hgu133plus2</td>
  410. <td>[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array</td>
  411. </tr>
  412. <tr>
  413. <td>GPL571</td>
  414. <td>hgu133a2</td>
  415. <td>[HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array</td>
  416. </tr>
  417. <tr>
  418. <td>GPL886</td>
  419. <td>hgug4111a</td>
  420. <td>Agilent-011871 Human 1B Microarray G4111A (Feature Number version)</td>
  421. </tr>
  422. <tr>
  423. <td>GPL887</td>
  424. <td>hgug4110b</td>
  425. <td>Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version)</td>
  426. </tr>
  427. <tr>
  428. <td>GPL1261</td>
  429. <td>mouse430a2</td>
  430. <td>[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array</td>
  431. </tr>
  432. <tr>
  433. <td>GPL1318</td>
  434. <td>xenopuslaevis</td>
  435. <td>[Xenopus_laevis] Affymetrix Xenopus laevis Genome Array</td>
  436. </tr>
  437. <tr>
  438. <td>GPL1319</td>
  439. <td>zebrafish</td>
  440. <td>[Zebrafish] Affymetrix Zebrafish Genome Array</td>
  441. </tr>
  442. <tr>
  443. <td>GPL1322</td>
  444. <td>drosophila2</td>
  445. <td>[Drosophila_2] Affymetrix Drosophila Genome 2.0 Array</td>
  446. </tr>
  447. <tr>
  448. <td>GPL1352</td>
  449. <td>u133x3p</td>
  450. <td>[U133_X3P] Affymetrix Human X3P Array</td>
  451. </tr>
  452. <tr>
  453. <td>GPL1355</td>
  454. <td>rat2302</td>
  455. <td>[Rat230_2] Affymetrix Rat Genome 230 2.0 Array</td>
  456. </tr>
  457. <tr>
  458. <td>GPL1708</td>
  459. <td>hgug4112a</td>
  460. <td>Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version)</td>
  461. </tr>
  462. <tr>
  463. <td>GPL2112</td>
  464. <td>bovine</td>
  465. <td>[Bovine] Affymetrix Bovine Genome Array</td>
  466. </tr>
  467. <tr>
  468. <td>GPL2529</td>
  469. <td>yeast2</td>
  470. <td>[Yeast_2] Affymetrix Yeast Genome 2.0 Array</td>
  471. </tr>
  472. <tr>
  473. <td>GPL2891</td>
  474. <td>h20kcod</td>
  475. <td>GE Healthcare/Amersham Biosciences CodeLink™ UniSet Human 20K I Bioarray</td>
  476. </tr>
  477. <tr>
  478. <td>GPL2898</td>
  479. <td>adme16cod</td>
  480. <td>GE Healthcare/Amersham Biosciences CodeLink™ ADME Rat 16-Assay Bioarray</td>
  481. </tr>
  482. <tr>
  483. <td>GPL3154</td>
  484. <td>ecoli2</td>
  485. <td>[E_coli_2] Affymetrix E. coli Genome 2.0 Array</td>
  486. </tr>
  487. <tr>
  488. <td>GPL3213</td>
  489. <td>chicken</td>
  490. <td>[Chicken] Affymetrix Chicken Genome Array</td>
  491. </tr>
  492. <tr>
  493. <td>GPL3533</td>
  494. <td>porcine</td>
  495. <td>[Porcine] Affymetrix Porcine Genome Array</td>
  496. </tr>
  497. <tr>
  498. <td>GPL3738</td>
  499. <td>canine2</td>
  500. <td>[Canine_2] Affymetrix Canine Genome 2.0 Array</td>
  501. </tr>
  502. <tr>
  503. <td>GPL3921</td>
  504. <td>hthgu133a</td>
  505. <td>[HT_HG-U133A] Affymetrix HT Human Genome U133A Array</td>
  506. </tr>
  507. <tr>
  508. <td>GPL3979</td>
  509. <td>canine</td>
  510. <td>[Canine] Affymetrix Canine Genome 1.0 Array</td>
  511. </tr>
  512. <tr>
  513. <td>GPL4032</td>
  514. <td></td>
  515. <td>[Maize] Affymetrix Maize Genome Array</td>
  516. </tr>
  517. <tr>
  518. <td>GPL4191</td>
  519. <td>h10kcod</td>
  520. <td>CodeLink UniSet Human I Bioarray</td>
  521. </tr>
  522. <tr>
  523. <td>GPL5188</td>
  524. <td>huex10sttranscriptcluster</td>
  525. <td>[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version]</td>
  526. </tr>
  527. <tr>
  528. <td>GPL5689</td>
  529. <td>hgug4100a</td>
  530. <td>Agilent Human 1 cDNA Microarray (G4100A) [layout C]</td>
  531. </tr>
  532. <tr>
  533. <td>GPL6097</td>
  534. <td>illuminaHumanv1</td>
  535. <td>Illumina human-6 v1.0 expression beadchip</td>
  536. </tr>
  537. <tr>
  538. <td>GPL6102</td>
  539. <td>illuminaHumanv2</td>
  540. <td>Illumina human-6 v2.0 expression beadchip</td>
  541. </tr>
  542. <tr>
  543. <td>GPL6244</td>
  544. <td>hugene10sttranscriptcluster</td>
  545. <td>[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]</td>
  546. </tr>
  547. <tr>
  548. <td>GPL6246</td>
  549. <td>mogene10sttranscriptcluster</td>
  550. <td>[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]</td>
  551. </tr>
  552. <tr>
  553. <td>GPL6885</td>
  554. <td>illuminaMousev2</td>
  555. <td>Illumina MouseRef-8 v2.0 expression beadchip</td>
  556. </tr>
  557. <tr>
  558. <td>GPL6947</td>
  559. <td>illuminaHumanv3</td>
  560. <td>Illumina HumanHT-12 V3.0 expression beadchip</td>
  561. </tr>
  562. <tr>
  563. <td>GPL8300</td>
  564. <td>hgu95av2</td>
  565. <td>[HG_U95Av2] Affymetrix Human Genome U95 Version 2 Array</td>
  566. </tr>
  567. <tr>
  568. <td>GPL8321</td>
  569. <td>mouse430a2</td>
  570. <td>[Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 Array</td>
  571. </tr>
  572. <tr>
  573. <td>GPL8490</td>
  574. <td>IlluminaHumanMethylation27k</td>
  575. <td>Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)</td>
  576. </tr>
  577. <tr>
  578. <td>GPL10558</td>
  579. <td>illuminaHumanv4</td>
  580. <td>Illumina HumanHT-12 V4.0 expression beadchip</td>
  581. </tr>
  582. <tr>
  583. <td>GPL11532</td>
  584. <td>hugene11sttranscriptcluster</td>
  585. <td>[HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [transcript (gene) version]</td>
  586. </tr>
  587. <tr>
  588. <td>GPL13497</td>
  589. <td>HsAgilentDesign026652</td>
  590. <td>Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Probe Name version)</td>
  591. </tr>
  592. <tr>
  593. <td>GPL13534</td>
  594. <td>IlluminaHumanMethylation450k</td>
  595. <td>Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)</td>
  596. </tr>
  597. <tr>
  598. <td>GPL13667</td>
  599. <td>hgu219</td>
  600. <td>[HG-U219] Affymetrix Human Genome U219 Array</td>
  601. </tr>
  602. <tr>
  603. <td>GPL14877</td>
  604. <td>hgu133plus2</td>
  605. <td>Affymetrix Human Genome U133 Plus 2.0 Array [Brainarray Version 13, HGU133Plus2_Hs_ENTREZG]</td>
  606. </tr>
  607. <tr>
  608. <td>GPL15380</td>
  609. <td>GGHumanMethCancerPanelv1</td>
  610. <td>Illumina Sentrix Array Matrix (SAM) - GoldenGate Methylation Cancer Panel I</td>
  611. </tr>
  612. <tr>
  613. <td>GPL15396</td>
  614. <td>hthgu133b</td>
  615. <td>[HT_HG-U133B] Affymetrix HT Human Genome U133B Array [custom CDF: ENTREZ brainarray v. 14]</td>
  616. </tr>
  617. <tr>
  618. <td>GPL17556</td>
  619. <td>hugene10sttranscriptcluster</td>
  620. <td>[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZG_17.0.0]</td>
  621. </tr>
  622. <tr>
  623. <td>GPL17897</td>
  624. <td>hthgu133a</td>
  625. <td>[HT_HG-U133A] Affymetrix Human Genome U133A Array (custom CDF: HTHGU133A_Hs_ENTREZG.cdf version 17.0.0)</td>
  626. </tr>
  627. <tr>
  628. <td>GPL18190</td>
  629. <td>hugene11sttranscriptcluster</td>
  630. <td>[HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [CDF: Brainarray HuGene11stv1_Hs_ENTREZG_15.1.0]</td>
  631. </tr>
  632. </tbody>
  633. </table>
  634. </div>
  635. <hr/>
  636. <div>
  637. <div class="post-metas my-3">
  638. <div class="post-meta">
  639. <i class="iconfont icon-tags"></i>
  640. <a href="/tags/oligo/" class="print-no-link">#oligo</a>
  641. <a href="/tags/GEO/" class="print-no-link">#GEO</a>
  642. <a href="/tags/ArrayExpress/" class="print-no-link">#ArrayExpress</a>
  643. </div>
  644. </div>
  645. <div class="license-box my-3">
  646. <div class="license-title">
  647. <div>【迁移】oligo:GEO/ArrayExpress芯片数据处理</div>
  648. <div>https://hexo.limour.top/oligo-GEO-ArrayExpress-xin-pian-shu-ju-chu-li</div>
  649. </div>
  650. <div class="license-meta">
  651. <div class="license-meta-item">
  652. <div>Author</div>
  653. <div>Limour</div>
  654. </div>
  655. <div class="license-meta-item license-meta-date">
  656. <div>Posted on</div>
  657. <div>July 29, 2022</div>
  658. </div>
  659. <div class="license-meta-item license-meta-date">
  660. <div>Updated on</div>
  661. <div>March 19, 2024</div>
  662. </div>
  663. <div class="license-meta-item">
  664. <div>Licensed under</div>
  665. <div>
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  687. <article class="post-prev col-6">
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