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  133. <h1 id="seo-header">oligo:GEO/ArrayExpress芯片数据处理</h1>
  134. <div class="markdown-body">
  135. <h2 id="conda配置环境"><a href="#conda配置环境" class="headerlink" title="conda配置环境"></a>conda配置环境</h2><ul>
  136. <li>conda clean -y -all</li>
  137. <li>conda create -n geo -c conda-forge r-base&#x3D;4.1.3</li>
  138. <li>conda activate geo</li>
  139. <li>conda install -c conda-forge r-tidyverse&#x3D;1.3.1 -y</li>
  140. <li>conda install -c conda-forge r-irkernel -y</li>
  141. <li>conda install -c conda-forge r-r.utils -y</li>
  142. <li>conda install -c conda-forge r-rcolorbrewer -y</li>
  143. <li>Rscript -e “IRkernel::installspec(name&#x3D;’geo’, displayname&#x3D;’r-geo’)”</li>
  144. <li>conda install -c bioconda bioconductor-geoquery -y</li>
  145. <li>conda install -c bioconda bioconductor-oligo -y</li>
  146. <li>conda install -c bioconda bioconductor-affy -y</li>
  147. <li>conda install -c bioconda bioconductor-pd.hugene.1.0.st.v1 -y # read.celfiles 需要啥<a target="_blank" rel="noopener" href="https://anaconda.org/bioconda/bioconductor-pd.hg.u133a.2">安装啥</a></li>
  148. <li>conda install -c bioconda bioconductor-pd.hg.u133a.2 -y</li>
  149. <li>conda install -c bioconda bioconductor-arrayexpress -y</li>
  150. <li>conda install -c bioconda bioconductor-biomart -y</li>
  151. <li>conda install -c bioconda bioconductor-affycoretools -y</li>
  152. </ul>
  153. <h2 id="下载芯片数据"><a href="#下载芯片数据" class="headerlink" title="下载芯片数据"></a>下载芯片数据</h2><h3 id="GEO"><a href="#GEO" class="headerlink" title="GEO"></a>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>
  154. <h3 id="ArrayExpress"><a href="#ArrayExpress" class="headerlink" title="ArrayExpress"></a>ArrayExpress</h3><ul>
  155. <li>~&#x2F;dev&#x2F;xray&#x2F;xray -c ~&#x2F;etc&#x2F;xui2.json &amp;</li>
  156. <li>wget -e “https_proxy&#x3D;<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>
  157. <li>unzip E-MEXP-1422.raw.1.zip</li>
  158. </ul>
  159. <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>
  160. <h2 id="RMA标准化数据"><a href="#RMA标准化数据" class="headerlink" title="RMA标准化数据"></a>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>
  161. <h2 id="探针转Symbol"><a href="#探针转Symbol" class="headerlink" title="探针转Symbol"></a>探针转Symbol</h2><ul>
  162. <li><a target="_blank" rel="noopener" href="https://occdn.limour.top/2157.html">f_dedup_IQR 函数来源</a></li>
  163. <li>data.raw@annotation 可以得到注释的包信息,如pd.hg.u133a.2</li>
  164. <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>
  165. <li>谷歌搜索 HG-U133A_2 + affymetrix,可以找到affymetrix官网对应的页面</li>
  166. <li>谷歌搜索 affymetrix “HG-U133A_2” site:<a target="_blank" rel="noopener" href="http://www.ncbi.nlm.nih.gov,随便进一个gse页面,找到对应的platforms,如/">www.ncbi.nlm.nih.gov,随便进一个GSE页面,找到对应的Platforms,如</a> GPL571 [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array,说明HG-U133A_2对应GPL571</li>
  167. </ul>
  168. <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>
  169. <h2 id="GPL与Platform对应表"><a href="#GPL与Platform对应表" class="headerlink" title="GPL与Platform对应表"></a>GPL与Platform对应表</h2><p>gpl</p>
  170. <p>bioc_package</p>
  171. <p>title</p>
  172. <p>GPL32</p>
  173. <p>mgu74a</p>
  174. <p>[MG_U74A] Affymetrix Murine Genome U74A Array</p>
  175. <p>GPL33</p>
  176. <p>mgu74b</p>
  177. <p>[MG_U74B] Affymetrix Murine Genome U74B Array</p>
  178. <p>GPL34</p>
  179. <p>mgu74c</p>
  180. <p>[MG_U74C] Affymetrix Murine Genome U74C Array</p>
  181. <p>GPL71</p>
  182. <p>ag</p>
  183. <p>[AG] Affymetrix Arabidopsis Genome Array</p>
  184. <p>GPL72</p>
  185. <p>drosgenome1</p>
  186. <p>[DrosGenome1] Affymetrix Drosophila Genome Array</p>
  187. <p>GPL74</p>
  188. <p>hcg110</p>
  189. <p>[HC_G110] Affymetrix Human Cancer Array</p>
  190. <p>GPL75</p>
  191. <p>mu11ksuba</p>
  192. <p>[Mu11KsubA] Affymetrix Murine 11K SubA Array</p>
  193. <p>GPL76</p>
  194. <p>mu11ksubb</p>
  195. <p>[Mu11KsubB] Affymetrix Murine 11K SubB Array</p>
  196. <p>GPL77</p>
  197. <p>mu19ksuba</p>
  198. <p>[Mu19KsubA] Affymetrix Murine 19K SubA Array</p>
  199. <p>GPL78</p>
  200. <p>mu19ksubb</p>
  201. <p>[Mu19KsubB] Affymetrix Murine 19K SubB Array</p>
  202. <p>GPL79</p>
  203. <p>mu19ksubc</p>
  204. <p>[Mu19KsubC] Affymetrix Murine 19K SubC Array</p>
  205. <p>GPL80</p>
  206. <p>hu6800</p>
  207. <p>[Hu6800] Affymetrix Human Full Length HuGeneFL Array</p>
  208. <p>GPL81</p>
  209. <p>mgu74av2</p>
  210. <p>[MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array</p>
  211. <p>GPL82</p>
  212. <p>mgu74bv2</p>
  213. <p>[MG_U74Bv2] Affymetrix Murine Genome U74B Version 2 Array</p>
  214. <p>GPL83</p>
  215. <p>mgu74cv2</p>
  216. <p>[MG_U74Cv2] Affymetrix Murine Genome U74 Version 2 Array</p>
  217. <p>GPL85</p>
  218. <p>rgu34a</p>
  219. <p>[RG_U34A] Affymetrix Rat Genome U34 Array</p>
  220. <p>GPL86</p>
  221. <p>rgu34b</p>
  222. <p>[RG_U34B] Affymetrix Rat Genome U34 Array</p>
  223. <p>GPL87</p>
  224. <p>rgu34c</p>
  225. <p>[RG_U34C] Affymetrix Rat Genome U34 Array</p>
  226. <p>GPL88</p>
  227. <p>rnu34</p>
  228. <p>[RN_U34] Affymetrix Rat Neurobiology U34 Array</p>
  229. <p>GPL89</p>
  230. <p>rtu34</p>
  231. <p>[RT_U34] Affymetrix Rat Toxicology U34 Array</p>
  232. <p>GPL90</p>
  233. <p>ygs98</p>
  234. <p>[YG_S98] Affymetrix Yeast Genome S98 Array</p>
  235. <p>GPL91</p>
  236. <p>hgu95av2</p>
  237. <p>[HG_U95A] Affymetrix Human Genome U95A Array</p>
  238. <p>GPL92</p>
  239. <p>hgu95b</p>
  240. <p>[HG_U95B] Affymetrix Human Genome U95B Array</p>
  241. <p>GPL93</p>
  242. <p>hgu95c</p>
  243. <p>[HG_U95C] Affymetrix Human Genome U95C Array</p>
  244. <p>GPL94</p>
  245. <p>hgu95d</p>
  246. <p>[HG_U95D] Affymetrix Human Genome U95D Array</p>
  247. <p>GPL95</p>
  248. <p>hgu95e</p>
  249. <p>[HG_U95E] Affymetrix Human Genome U95E Array</p>
  250. <p>GPL96</p>
  251. <p>hgu133a</p>
  252. <p>[HG-U133A] Affymetrix Human Genome U133A Array</p>
  253. <p>GPL97</p>
  254. <p>hgu133b</p>
  255. <p>[HG-U133B] Affymetrix Human Genome U133B Array</p>
  256. <p>GPL98</p>
  257. <p>hu35ksuba</p>
  258. <p>[Hu35KsubA] Affymetrix Human 35K SubA Array</p>
  259. <p>GPL99</p>
  260. <p>hu35ksubb</p>
  261. <p>[Hu35KsubB] Affymetrix Human 35K SubB Array</p>
  262. <p>GPL100</p>
  263. <p>hu35ksubc</p>
  264. <p>[Hu35KsubC] Affymetrix Human 35K SubC Array</p>
  265. <p>GPL101</p>
  266. <p>hu35ksubd</p>
  267. <p>[Hu35KsubD] Affymetrix Human 35K SubD Array</p>
  268. <p>GPL198</p>
  269. <p>ath1121501</p>
  270. <p>[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array</p>
  271. <p>GPL199</p>
  272. <p>ecoli2</p>
  273. <p>[Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array</p>
  274. <p>GPL200</p>
  275. <p>celegans</p>
  276. <p>[Celegans] Affymetrix C. elegans Genome Array</p>
  277. <p>GPL201</p>
  278. <p>hgfocus</p>
  279. <p>[HG-Focus] Affymetrix Human HG-Focus Target Array</p>
  280. <p>GPL339</p>
  281. <p>moe430a</p>
  282. <p>[MOE430A] Affymetrix Mouse Expression 430A Array</p>
  283. <p>GPL340</p>
  284. <p>mouse4302</p>
  285. <p>[MOE430B] Affymetrix Mouse Expression 430B Array</p>
  286. <p>GPL341</p>
  287. <p>rae230a</p>
  288. <p>[RAE230A] Affymetrix Rat Expression 230A Array</p>
  289. <p>GPL342</p>
  290. <p>rae230b</p>
  291. <p>[RAE230B] Affymetrix Rat Expression 230B Array</p>
  292. <p>GPL570</p>
  293. <p>hgu133plus2</p>
  294. <p>[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array</p>
  295. <p>GPL571</p>
  296. <p>hgu133a2</p>
  297. <p>[HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array</p>
  298. <p>GPL886</p>
  299. <p>hgug4111a</p>
  300. <p>Agilent-011871 Human 1B Microarray G4111A (Feature Number version)</p>
  301. <p>GPL887</p>
  302. <p>hgug4110b</p>
  303. <p>Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version)</p>
  304. <p>GPL1261</p>
  305. <p>mouse430a2</p>
  306. <p>[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array</p>
  307. <p>GPL1318</p>
  308. <p>xenopuslaevis</p>
  309. <p>[Xenopus_laevis] Affymetrix Xenopus laevis Genome Array</p>
  310. <p>GPL1319</p>
  311. <p>zebrafish</p>
  312. <p>[Zebrafish] Affymetrix Zebrafish Genome Array</p>
  313. <p>GPL1322</p>
  314. <p>drosophila2</p>
  315. <p>[Drosophila_2] Affymetrix Drosophila Genome 2.0 Array</p>
  316. <p>GPL1352</p>
  317. <p>u133x3p</p>
  318. <p>[U133_X3P] Affymetrix Human X3P Array</p>
  319. <p>GPL1355</p>
  320. <p>rat2302</p>
  321. <p>[Rat230_2] Affymetrix Rat Genome 230 2.0 Array</p>
  322. <p>GPL1708</p>
  323. <p>hgug4112a</p>
  324. <p>Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version)</p>
  325. <p>GPL2112</p>
  326. <p>bovine</p>
  327. <p>[Bovine] Affymetrix Bovine Genome Array</p>
  328. <p>GPL2529</p>
  329. <p>yeast2</p>
  330. <p>[Yeast_2] Affymetrix Yeast Genome 2.0 Array</p>
  331. <p>GPL2891</p>
  332. <p>h20kcod</p>
  333. <p>GE Healthcare&#x2F;Amersham Biosciences CodeLink™ UniSet Human 20K I Bioarray</p>
  334. <p>GPL2898</p>
  335. <p>adme16cod</p>
  336. <p>GE Healthcare&#x2F;Amersham Biosciences CodeLink™ ADME Rat 16-Assay Bioarray</p>
  337. <p>GPL3154</p>
  338. <p>ecoli2</p>
  339. <p>[E_coli_2] Affymetrix E. coli Genome 2.0 Array</p>
  340. <p>GPL3213</p>
  341. <p>chicken</p>
  342. <p>[Chicken] Affymetrix Chicken Genome Array</p>
  343. <p>GPL3533</p>
  344. <p>porcine</p>
  345. <p>[Porcine] Affymetrix Porcine Genome Array</p>
  346. <p>GPL3738</p>
  347. <p>canine2</p>
  348. <p>[Canine_2] Affymetrix Canine Genome 2.0 Array</p>
  349. <p>GPL3921</p>
  350. <p>hthgu133a</p>
  351. <p>[HT_HG-U133A] Affymetrix HT Human Genome U133A Array</p>
  352. <p>GPL3979</p>
  353. <p>canine</p>
  354. <p>[Canine] Affymetrix Canine Genome 1.0 Array</p>
  355. <p>GPL4032</p>
  356. <p>[Maize] Affymetrix Maize Genome Array</p>
  357. <p>GPL4191</p>
  358. <p>h10kcod</p>
  359. <p>CodeLink UniSet Human I Bioarray</p>
  360. <p>GPL5188</p>
  361. <p>huex10sttranscriptcluster</p>
  362. <p>[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version]</p>
  363. <p>GPL5689</p>
  364. <p>hgug4100a</p>
  365. <p>Agilent Human 1 cDNA Microarray (G4100A) [layout C]</p>
  366. <p>GPL6097</p>
  367. <p>illuminaHumanv1</p>
  368. <p>Illumina human-6 v1.0 expression beadchip</p>
  369. <p>GPL6102</p>
  370. <p>illuminaHumanv2</p>
  371. <p>Illumina human-6 v2.0 expression beadchip</p>
  372. <p>GPL6244</p>
  373. <p>hugene10sttranscriptcluster</p>
  374. <p>[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]</p>
  375. <p>GPL6246</p>
  376. <p>mogene10sttranscriptcluster</p>
  377. <p>[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]</p>
  378. <p>GPL6885</p>
  379. <p>illuminaMousev2</p>
  380. <p>Illumina MouseRef-8 v2.0 expression beadchip</p>
  381. <p>GPL6947</p>
  382. <p>illuminaHumanv3</p>
  383. <p>Illumina HumanHT-12 V3.0 expression beadchip</p>
  384. <p>GPL8300</p>
  385. <p>hgu95av2</p>
  386. <p>[HG_U95Av2] Affymetrix Human Genome U95 Version 2 Array</p>
  387. <p>GPL8321</p>
  388. <p>mouse430a2</p>
  389. <p>[Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 Array</p>
  390. <p>GPL8490</p>
  391. <p>IlluminaHumanMethylation27k</p>
  392. <p>Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)</p>
  393. <p>GPL10558</p>
  394. <p>illuminaHumanv4</p>
  395. <p>Illumina HumanHT-12 V4.0 expression beadchip</p>
  396. <p>GPL11532</p>
  397. <p>hugene11sttranscriptcluster</p>
  398. <p>[HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [transcript (gene) version]</p>
  399. <p>GPL13497</p>
  400. <p>HsAgilentDesign026652</p>
  401. <p>Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Probe Name version)</p>
  402. <p>GPL13534</p>
  403. <p>IlluminaHumanMethylation450k</p>
  404. <p>Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)</p>
  405. <p>GPL13667</p>
  406. <p>hgu219</p>
  407. <p>[HG-U219] Affymetrix Human Genome U219 Array</p>
  408. <p>GPL14877</p>
  409. <p>hgu133plus2</p>
  410. <p>Affymetrix Human Genome U133 Plus 2.0 Array [Brainarray Version 13, HGU133Plus2_Hs_ENTREZG]</p>
  411. <p>GPL15380</p>
  412. <p>GGHumanMethCancerPanelv1</p>
  413. <p>Illumina Sentrix Array Matrix (SAM) - GoldenGate Methylation Cancer Panel I</p>
  414. <p>GPL15396</p>
  415. <p>hthgu133b</p>
  416. <p>[HT_HG-U133B] Affymetrix HT Human Genome U133B Array [custom CDF: ENTREZ brainarray v. 14]</p>
  417. <p>GPL17556</p>
  418. <p>hugene10sttranscriptcluster</p>
  419. <p>[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZG_17.0.0]</p>
  420. <p>GPL17897</p>
  421. <p>hthgu133a</p>
  422. <p>[HT_HG-U133A] Affymetrix Human Genome U133A Array (custom CDF: HTHGU133A_Hs_ENTREZG.cdf version 17.0.0)</p>
  423. <p>GPL18190</p>
  424. <p>hugene11sttranscriptcluster</p>
  425. <p>[HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [CDF: Brainarray HuGene11stv1_Hs_ENTREZG_15.1.0]</p>
  426. <p>来自:<a target="_blank" rel="noopener" href="https://icode.best/i/32522930456304">爱代码爱编程</a></p>
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