newdata.ipynb

{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 下载数据\n",
    "\n",
    "下载 https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE162330&format=file&file=GSE162330%5Fre%2Danalyzed%5FIllumina%5Fdata%2Etxt%2Egz 并解压至 ./datasets 目录\n",
    "\n",
    "下载 https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE162330&format=file&file=GSE162330%5Fre%2Danalyzed%5Fsample%5Freferences%2Etxt%2Egz 并解压至 ./datasets 目录, 手动删除第一行内容"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th>ID_REF</th>\n",
       "      <th>SLC35E2</th>\n",
       "      <th>EFCAB1</th>\n",
       "      <th>IPO13</th>\n",
       "      <th>PRSS41</th>\n",
       "      <th>FAM86FP</th>\n",
       "      <th>CDT1</th>\n",
       "      <th>LPP</th>\n",
       "      <th>HNRNPAB</th>\n",
       "      <th>BORCS5</th>\n",
       "      <th>SNIP1</th>\n",
       "      <th>...</th>\n",
       "      <th>KCNQ4</th>\n",
       "      <th>SYNRG</th>\n",
       "      <th>HS6ST2</th>\n",
       "      <th>KIR2DL5A</th>\n",
       "      <th>KIR2DL5A;KIR2DL5B</th>\n",
       "      <th>WSB1</th>\n",
       "      <th>CD96</th>\n",
       "      <th>ENOX2</th>\n",
       "      <th>THOC3</th>\n",
       "      <th>CFAP74</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>GSM812741</th>\n",
       "      <td>57.343344</td>\n",
       "      <td>69.296670</td>\n",
       "      <td>183.254432</td>\n",
       "      <td>57.573006</td>\n",
       "      <td>83.790153</td>\n",
       "      <td>156.001181</td>\n",
       "      <td>987.872660</td>\n",
       "      <td>1947.750743</td>\n",
       "      <td>62.482761</td>\n",
       "      <td>262.762322</td>\n",
       "      <td>...</td>\n",
       "      <td>72.952503</td>\n",
       "      <td>100.944595</td>\n",
       "      <td>63.233187</td>\n",
       "      <td>71.608758</td>\n",
       "      <td>76.356009</td>\n",
       "      <td>552.453792</td>\n",
       "      <td>245.857856</td>\n",
       "      <td>119.607471</td>\n",
       "      <td>198.064438</td>\n",
       "      <td>1904.233487</td>\n",
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       "    <tr>\n",
       "      <th>GSM812742</th>\n",
       "      <td>69.705089</td>\n",
       "      <td>79.282110</td>\n",
       "      <td>183.333693</td>\n",
       "      <td>64.120652</td>\n",
       "      <td>82.326561</td>\n",
       "      <td>145.230038</td>\n",
       "      <td>998.672568</td>\n",
       "      <td>1843.449973</td>\n",
       "      <td>69.794561</td>\n",
       "      <td>259.302232</td>\n",
       "      <td>...</td>\n",
       "      <td>71.536205</td>\n",
       "      <td>116.458835</td>\n",
       "      <td>72.315498</td>\n",
       "      <td>79.410070</td>\n",
       "      <td>83.221108</td>\n",
       "      <td>548.973943</td>\n",
       "      <td>229.253279</td>\n",
       "      <td>116.621511</td>\n",
       "      <td>175.772373</td>\n",
       "      <td>2081.254881</td>\n",
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       "    <tr>\n",
       "      <th>GSM812743</th>\n",
       "      <td>73.036540</td>\n",
       "      <td>89.164946</td>\n",
       "      <td>180.887642</td>\n",
       "      <td>61.611988</td>\n",
       "      <td>86.262390</td>\n",
       "      <td>155.078176</td>\n",
       "      <td>990.188262</td>\n",
       "      <td>1899.100435</td>\n",
       "      <td>61.481366</td>\n",
       "      <td>256.649928</td>\n",
       "      <td>...</td>\n",
       "      <td>76.827521</td>\n",
       "      <td>114.205173</td>\n",
       "      <td>63.684281</td>\n",
       "      <td>72.892388</td>\n",
       "      <td>80.334527</td>\n",
       "      <td>561.296577</td>\n",
       "      <td>243.264161</td>\n",
       "      <td>115.032853</td>\n",
       "      <td>188.609068</td>\n",
       "      <td>2023.171144</td>\n",
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       "    <tr>\n",
       "      <th>GSM812744</th>\n",
       "      <td>78.463588</td>\n",
       "      <td>77.619671</td>\n",
       "      <td>174.732394</td>\n",
       "      <td>74.987394</td>\n",
       "      <td>85.844520</td>\n",
       "      <td>156.776927</td>\n",
       "      <td>1024.182083</td>\n",
       "      <td>1933.960576</td>\n",
       "      <td>64.047508</td>\n",
       "      <td>268.887371</td>\n",
       "      <td>...</td>\n",
       "      <td>75.479526</td>\n",
       "      <td>93.654982</td>\n",
       "      <td>64.940628</td>\n",
       "      <td>78.741397</td>\n",
       "      <td>79.502031</td>\n",
       "      <td>558.772205</td>\n",
       "      <td>239.574571</td>\n",
       "      <td>119.360743</td>\n",
       "      <td>188.619845</td>\n",
       "      <td>2131.440755</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GSM812745</th>\n",
       "      <td>70.075808</td>\n",
       "      <td>86.119485</td>\n",
       "      <td>209.510081</td>\n",
       "      <td>68.950055</td>\n",
       "      <td>84.869570</td>\n",
       "      <td>173.577397</td>\n",
       "      <td>955.366767</td>\n",
       "      <td>2038.549693</td>\n",
       "      <td>65.759330</td>\n",
       "      <td>226.748612</td>\n",
       "      <td>...</td>\n",
       "      <td>81.383143</td>\n",
       "      <td>104.016101</td>\n",
       "      <td>58.478697</td>\n",
       "      <td>77.837236</td>\n",
       "      <td>77.153573</td>\n",
       "      <td>456.100476</td>\n",
       "      <td>243.985245</td>\n",
       "      <td>72.487223</td>\n",
       "      <td>239.305480</td>\n",
       "      <td>1342.764020</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>GSM992813</th>\n",
       "      <td>84.641542</td>\n",
       "      <td>83.620861</td>\n",
       "      <td>136.805555</td>\n",
       "      <td>58.864421</td>\n",
       "      <td>69.495324</td>\n",
       "      <td>67.320314</td>\n",
       "      <td>1422.832383</td>\n",
       "      <td>1078.551986</td>\n",
       "      <td>48.584998</td>\n",
       "      <td>245.502686</td>\n",
       "      <td>...</td>\n",
       "      <td>75.598463</td>\n",
       "      <td>141.629992</td>\n",
       "      <td>64.298581</td>\n",
       "      <td>90.252188</td>\n",
       "      <td>82.979899</td>\n",
       "      <td>1009.900189</td>\n",
       "      <td>711.119398</td>\n",
       "      <td>102.673638</td>\n",
       "      <td>110.402345</td>\n",
       "      <td>1552.190592</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GSM992814</th>\n",
       "      <td>72.952676</td>\n",
       "      <td>88.635824</td>\n",
       "      <td>166.329932</td>\n",
       "      <td>84.330231</td>\n",
       "      <td>74.683467</td>\n",
       "      <td>73.794173</td>\n",
       "      <td>1236.940166</td>\n",
       "      <td>1385.575874</td>\n",
       "      <td>50.097198</td>\n",
       "      <td>235.203057</td>\n",
       "      <td>...</td>\n",
       "      <td>78.454266</td>\n",
       "      <td>127.806996</td>\n",
       "      <td>55.808772</td>\n",
       "      <td>91.848929</td>\n",
       "      <td>118.586502</td>\n",
       "      <td>919.158595</td>\n",
       "      <td>537.841773</td>\n",
       "      <td>93.214727</td>\n",
       "      <td>132.976823</td>\n",
       "      <td>2241.921425</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GSM992815</th>\n",
       "      <td>68.921252</td>\n",
       "      <td>82.203676</td>\n",
       "      <td>155.466723</td>\n",
       "      <td>56.275146</td>\n",
       "      <td>67.538536</td>\n",
       "      <td>80.415349</td>\n",
       "      <td>1194.316919</td>\n",
       "      <td>1357.964453</td>\n",
       "      <td>59.279074</td>\n",
       "      <td>196.130623</td>\n",
       "      <td>...</td>\n",
       "      <td>51.244135</td>\n",
       "      <td>103.508612</td>\n",
       "      <td>70.966438</td>\n",
       "      <td>74.287780</td>\n",
       "      <td>112.830477</td>\n",
       "      <td>1025.690677</td>\n",
       "      <td>510.220834</td>\n",
       "      <td>89.504170</td>\n",
       "      <td>116.333114</td>\n",
       "      <td>1468.777349</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GSM992816</th>\n",
       "      <td>85.498310</td>\n",
       "      <td>82.215129</td>\n",
       "      <td>131.070209</td>\n",
       "      <td>67.445440</td>\n",
       "      <td>82.107892</td>\n",
       "      <td>86.164220</td>\n",
       "      <td>1237.712050</td>\n",
       "      <td>1128.038037</td>\n",
       "      <td>46.278333</td>\n",
       "      <td>268.637146</td>\n",
       "      <td>...</td>\n",
       "      <td>79.818817</td>\n",
       "      <td>126.135451</td>\n",
       "      <td>35.164529</td>\n",
       "      <td>76.871664</td>\n",
       "      <td>92.280377</td>\n",
       "      <td>1016.099523</td>\n",
       "      <td>648.236300</td>\n",
       "      <td>96.951412</td>\n",
       "      <td>100.408598</td>\n",
       "      <td>1854.712685</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GSM992817</th>\n",
       "      <td>81.645304</td>\n",
       "      <td>78.309911</td>\n",
       "      <td>143.323563</td>\n",
       "      <td>63.569331</td>\n",
       "      <td>90.809920</td>\n",
       "      <td>54.676879</td>\n",
       "      <td>1375.976390</td>\n",
       "      <td>843.324466</td>\n",
       "      <td>74.511954</td>\n",
       "      <td>251.109883</td>\n",
       "      <td>...</td>\n",
       "      <td>67.511155</td>\n",
       "      <td>146.175326</td>\n",
       "      <td>58.329953</td>\n",
       "      <td>92.938406</td>\n",
       "      <td>82.684672</td>\n",
       "      <td>934.163975</td>\n",
       "      <td>668.799519</td>\n",
       "      <td>94.814842</td>\n",
       "      <td>138.795502</td>\n",
       "      <td>2335.231725</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1751 rows × 19947 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "ID_REF       SLC35E2     EFCAB1       IPO13     PRSS41    FAM86FP        CDT1  \\\n",
       "GSM812741  57.343344  69.296670  183.254432  57.573006  83.790153  156.001181   \n",
       "GSM812742  69.705089  79.282110  183.333693  64.120652  82.326561  145.230038   \n",
       "GSM812743  73.036540  89.164946  180.887642  61.611988  86.262390  155.078176   \n",
       "GSM812744  78.463588  77.619671  174.732394  74.987394  85.844520  156.776927   \n",
       "GSM812745  70.075808  86.119485  209.510081  68.950055  84.869570  173.577397   \n",
       "...              ...        ...         ...        ...        ...         ...   \n",
       "GSM992813  84.641542  83.620861  136.805555  58.864421  69.495324   67.320314   \n",
       "GSM992814  72.952676  88.635824  166.329932  84.330231  74.683467   73.794173   \n",
       "GSM992815  68.921252  82.203676  155.466723  56.275146  67.538536   80.415349   \n",
       "GSM992816  85.498310  82.215129  131.070209  67.445440  82.107892   86.164220   \n",
       "GSM992817  81.645304  78.309911  143.323563  63.569331  90.809920   54.676879   \n",
       "\n",
       "ID_REF             LPP      HNRNPAB     BORCS5       SNIP1  ...      KCNQ4  \\\n",
       "GSM812741   987.872660  1947.750743  62.482761  262.762322  ...  72.952503   \n",
       "GSM812742   998.672568  1843.449973  69.794561  259.302232  ...  71.536205   \n",
       "GSM812743   990.188262  1899.100435  61.481366  256.649928  ...  76.827521   \n",
       "GSM812744  1024.182083  1933.960576  64.047508  268.887371  ...  75.479526   \n",
       "GSM812745   955.366767  2038.549693  65.759330  226.748612  ...  81.383143   \n",
       "...                ...          ...        ...         ...  ...        ...   \n",
       "GSM992813  1422.832383  1078.551986  48.584998  245.502686  ...  75.598463   \n",
       "GSM992814  1236.940166  1385.575874  50.097198  235.203057  ...  78.454266   \n",
       "GSM992815  1194.316919  1357.964453  59.279074  196.130623  ...  51.244135   \n",
       "GSM992816  1237.712050  1128.038037  46.278333  268.637146  ...  79.818817   \n",
       "GSM992817  1375.976390   843.324466  74.511954  251.109883  ...  67.511155   \n",
       "\n",
       "ID_REF          SYNRG     HS6ST2   KIR2DL5A  KIR2DL5A;KIR2DL5B         WSB1  \\\n",
       "GSM812741  100.944595  63.233187  71.608758          76.356009   552.453792   \n",
       "GSM812742  116.458835  72.315498  79.410070          83.221108   548.973943   \n",
       "GSM812743  114.205173  63.684281  72.892388          80.334527   561.296577   \n",
       "GSM812744   93.654982  64.940628  78.741397          79.502031   558.772205   \n",
       "GSM812745  104.016101  58.478697  77.837236          77.153573   456.100476   \n",
       "...               ...        ...        ...                ...          ...   \n",
       "GSM992813  141.629992  64.298581  90.252188          82.979899  1009.900189   \n",
       "GSM992814  127.806996  55.808772  91.848929         118.586502   919.158595   \n",
       "GSM992815  103.508612  70.966438  74.287780         112.830477  1025.690677   \n",
       "GSM992816  126.135451  35.164529  76.871664          92.280377  1016.099523   \n",
       "GSM992817  146.175326  58.329953  92.938406          82.684672   934.163975   \n",
       "\n",
       "ID_REF           CD96       ENOX2       THOC3       CFAP74  \n",
       "GSM812741  245.857856  119.607471  198.064438  1904.233487  \n",
       "GSM812742  229.253279  116.621511  175.772373  2081.254881  \n",
       "GSM812743  243.264161  115.032853  188.609068  2023.171144  \n",
       "GSM812744  239.574571  119.360743  188.619845  2131.440755  \n",
       "GSM812745  243.985245   72.487223  239.305480  1342.764020  \n",
       "...               ...         ...         ...          ...  \n",
       "GSM992813  711.119398  102.673638  110.402345  1552.190592  \n",
       "GSM992814  537.841773   93.214727  132.976823  2241.921425  \n",
       "GSM992815  510.220834   89.504170  116.333114  1468.777349  \n",
       "GSM992816  648.236300   96.951412  100.408598  1854.712685  \n",
       "GSM992817  668.799519   94.814842  138.795502  2335.231725  \n",
       "\n",
       "[1751 rows x 19947 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import pandas as pd\n",
    "sample_csv = 2**pd.read_csv('./datasets/GSE162330_re-analyzed_Illumina_data.csv',\n",
    "                            sep='\\t',\n",
    "                            index_col=0,\n",
    "                            ).T\n",
    "reference_csv = pd.read_csv('./datasets/GSE162330_re-analyzed_sample_references.csv',sep='\\t')\n",
    "sample_csv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Sample name</th>\n",
       "      <th>organism</th>\n",
       "      <th>characteristics: sample class</th>\n",
       "      <th>description</th>\n",
       "      <th>chip name or GEO platform id</th>\n",
       "      <th>Unnamed: 5</th>\n",
       "      <th>Unnamed: 6</th>\n",
       "      <th>Unnamed: 7</th>\n",
       "      <th>Unnamed: 8</th>\n",
       "      <th>Unnamed: 9</th>\n",
       "      <th>...</th>\n",
       "      <th>KCNQ4</th>\n",
       "      <th>SYNRG</th>\n",
       "      <th>HS6ST2</th>\n",
       "      <th>KIR2DL5A</th>\n",
       "      <th>KIR2DL5A;KIR2DL5B</th>\n",
       "      <th>WSB1</th>\n",
       "      <th>CD96</th>\n",
       "      <th>ENOX2</th>\n",
       "      <th>THOC3</th>\n",
       "      <th>CFAP74</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GSM812741</td>\n",
       "      <td>control</td>\n",
       "      <td>c</td>\n",
       "      <td>GSE32707</td>\n",
       "      <td>GPL10558</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>72.952503</td>\n",
       "      <td>100.944595</td>\n",
       "      <td>63.233187</td>\n",
       "      <td>71.608758</td>\n",
       "      <td>76.356009</td>\n",
       "      <td>552.453792</td>\n",
       "      <td>245.857856</td>\n",
       "      <td>119.607471</td>\n",
       "      <td>198.064438</td>\n",
       "      <td>1904.233487</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>GSM812742</td>\n",
       "      <td>control</td>\n",
       "      <td>c</td>\n",
       "      <td>GSE32707</td>\n",
       "      <td>GPL10558</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>71.536205</td>\n",
       "      <td>116.458835</td>\n",
       "      <td>72.315498</td>\n",
       "      <td>79.410070</td>\n",
       "      <td>83.221108</td>\n",
       "      <td>548.973943</td>\n",
       "      <td>229.253279</td>\n",
       "      <td>116.621511</td>\n",
       "      <td>175.772373</td>\n",
       "      <td>2081.254881</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>GSM812743</td>\n",
       "      <td>control</td>\n",
       "      <td>c</td>\n",
       "      <td>GSE32707</td>\n",
       "      <td>GPL10558</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>76.827521</td>\n",
       "      <td>114.205173</td>\n",
       "      <td>63.684281</td>\n",
       "      <td>72.892388</td>\n",
       "      <td>80.334527</td>\n",
       "      <td>561.296577</td>\n",
       "      <td>243.264161</td>\n",
       "      <td>115.032853</td>\n",
       "      <td>188.609068</td>\n",
       "      <td>2023.171144</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GSM812744</td>\n",
       "      <td>control</td>\n",
       "      <td>c</td>\n",
       "      <td>GSE32707</td>\n",
       "      <td>GPL10558</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>75.479526</td>\n",
       "      <td>93.654982</td>\n",
       "      <td>64.940628</td>\n",
       "      <td>78.741397</td>\n",
       "      <td>79.502031</td>\n",
       "      <td>558.772205</td>\n",
       "      <td>239.574571</td>\n",
       "      <td>119.360743</td>\n",
       "      <td>188.619845</td>\n",
       "      <td>2131.440755</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GSM812745</td>\n",
       "      <td>control</td>\n",
       "      <td>c</td>\n",
       "      <td>GSE32707</td>\n",
       "      <td>GPL10558</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>81.383143</td>\n",
       "      <td>104.016101</td>\n",
       "      <td>58.478697</td>\n",
       "      <td>77.837236</td>\n",
       "      <td>77.153573</td>\n",
       "      <td>456.100476</td>\n",
       "      <td>243.985245</td>\n",
       "      <td>72.487223</td>\n",
       "      <td>239.305480</td>\n",
       "      <td>1342.764020</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1746</th>\n",
       "      <td>GSM992813</td>\n",
       "      <td>control</td>\n",
       "      <td>c</td>\n",
       "      <td>GSE40396</td>\n",
       "      <td>GPL10558</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>75.598463</td>\n",
       "      <td>141.629992</td>\n",
       "      <td>64.298581</td>\n",
       "      <td>90.252188</td>\n",
       "      <td>82.979899</td>\n",
       "      <td>1009.900189</td>\n",
       "      <td>711.119398</td>\n",
       "      <td>102.673638</td>\n",
       "      <td>110.402345</td>\n",
       "      <td>1552.190592</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1747</th>\n",
       "      <td>GSM992814</td>\n",
       "      <td>control</td>\n",
       "      <td>c</td>\n",
       "      <td>GSE40396</td>\n",
       "      <td>GPL10558</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>78.454266</td>\n",
       "      <td>127.806996</td>\n",
       "      <td>55.808772</td>\n",
       "      <td>91.848929</td>\n",
       "      <td>118.586502</td>\n",
       "      <td>919.158595</td>\n",
       "      <td>537.841773</td>\n",
       "      <td>93.214727</td>\n",
       "      <td>132.976823</td>\n",
       "      <td>2241.921425</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1748</th>\n",
       "      <td>GSM992815</td>\n",
       "      <td>control</td>\n",
       "      <td>c</td>\n",
       "      <td>GSE40396</td>\n",
       "      <td>GPL10558</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>51.244135</td>\n",
       "      <td>103.508612</td>\n",
       "      <td>70.966438</td>\n",
       "      <td>74.287780</td>\n",
       "      <td>112.830477</td>\n",
       "      <td>1025.690677</td>\n",
       "      <td>510.220834</td>\n",
       "      <td>89.504170</td>\n",
       "      <td>116.333114</td>\n",
       "      <td>1468.777349</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1749</th>\n",
       "      <td>GSM992816</td>\n",
       "      <td>control</td>\n",
       "      <td>c</td>\n",
       "      <td>GSE40396</td>\n",
       "      <td>GPL10558</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>79.818817</td>\n",
       "      <td>126.135451</td>\n",
       "      <td>35.164529</td>\n",
       "      <td>76.871664</td>\n",
       "      <td>92.280377</td>\n",
       "      <td>1016.099523</td>\n",
       "      <td>648.236300</td>\n",
       "      <td>96.951412</td>\n",
       "      <td>100.408598</td>\n",
       "      <td>1854.712685</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1750</th>\n",
       "      <td>GSM992817</td>\n",
       "      <td>control</td>\n",
       "      <td>c</td>\n",
       "      <td>GSE40396</td>\n",
       "      <td>GPL10558</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>67.511155</td>\n",
       "      <td>146.175326</td>\n",
       "      <td>58.329953</td>\n",
       "      <td>92.938406</td>\n",
       "      <td>82.684672</td>\n",
       "      <td>934.163975</td>\n",
       "      <td>668.799519</td>\n",
       "      <td>94.814842</td>\n",
       "      <td>138.795502</td>\n",
       "      <td>2335.231725</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1751 rows × 19957 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     Sample name organism characteristics: sample class description  \\\n",
       "0      GSM812741  control                             c    GSE32707   \n",
       "1      GSM812742  control                             c    GSE32707   \n",
       "2      GSM812743  control                             c    GSE32707   \n",
       "3      GSM812744  control                             c    GSE32707   \n",
       "4      GSM812745  control                             c    GSE32707   \n",
       "...          ...      ...                           ...         ...   \n",
       "1746   GSM992813  control                             c    GSE40396   \n",
       "1747   GSM992814  control                             c    GSE40396   \n",
       "1748   GSM992815  control                             c    GSE40396   \n",
       "1749   GSM992816  control                             c    GSE40396   \n",
       "1750   GSM992817  control                             c    GSE40396   \n",
       "\n",
       "     chip name or GEO platform id  Unnamed: 5  Unnamed: 6  Unnamed: 7  \\\n",
       "0                        GPL10558         NaN         NaN         NaN   \n",
       "1                        GPL10558         NaN         NaN         NaN   \n",
       "2                        GPL10558         NaN         NaN         NaN   \n",
       "3                        GPL10558         NaN         NaN         NaN   \n",
       "4                        GPL10558         NaN         NaN         NaN   \n",
       "...                           ...         ...         ...         ...   \n",
       "1746                     GPL10558         NaN         NaN         NaN   \n",
       "1747                     GPL10558         NaN         NaN         NaN   \n",
       "1748                     GPL10558         NaN         NaN         NaN   \n",
       "1749                     GPL10558         NaN         NaN         NaN   \n",
       "1750                     GPL10558         NaN         NaN         NaN   \n",
       "\n",
       "      Unnamed: 8  Unnamed: 9  ...      KCNQ4       SYNRG     HS6ST2  \\\n",
       "0            NaN         NaN  ...  72.952503  100.944595  63.233187   \n",
       "1            NaN         NaN  ...  71.536205  116.458835  72.315498   \n",
       "2            NaN         NaN  ...  76.827521  114.205173  63.684281   \n",
       "3            NaN         NaN  ...  75.479526   93.654982  64.940628   \n",
       "4            NaN         NaN  ...  81.383143  104.016101  58.478697   \n",
       "...          ...         ...  ...        ...         ...        ...   \n",
       "1746         NaN         NaN  ...  75.598463  141.629992  64.298581   \n",
       "1747         NaN         NaN  ...  78.454266  127.806996  55.808772   \n",
       "1748         NaN         NaN  ...  51.244135  103.508612  70.966438   \n",
       "1749         NaN         NaN  ...  79.818817  126.135451  35.164529   \n",
       "1750         NaN         NaN  ...  67.511155  146.175326  58.329953   \n",
       "\n",
       "       KIR2DL5A  KIR2DL5A;KIR2DL5B         WSB1        CD96       ENOX2  \\\n",
       "0     71.608758          76.356009   552.453792  245.857856  119.607471   \n",
       "1     79.410070          83.221108   548.973943  229.253279  116.621511   \n",
       "2     72.892388          80.334527   561.296577  243.264161  115.032853   \n",
       "3     78.741397          79.502031   558.772205  239.574571  119.360743   \n",
       "4     77.837236          77.153573   456.100476  243.985245   72.487223   \n",
       "...         ...                ...          ...         ...         ...   \n",
       "1746  90.252188          82.979899  1009.900189  711.119398  102.673638   \n",
       "1747  91.848929         118.586502   919.158595  537.841773   93.214727   \n",
       "1748  74.287780         112.830477  1025.690677  510.220834   89.504170   \n",
       "1749  76.871664          92.280377  1016.099523  648.236300   96.951412   \n",
       "1750  92.938406          82.684672   934.163975  668.799519   94.814842   \n",
       "\n",
       "           THOC3       CFAP74  \n",
       "0     198.064438  1904.233487  \n",
       "1     175.772373  2081.254881  \n",
       "2     188.609068  2023.171144  \n",
       "3     188.619845  2131.440755  \n",
       "4     239.305480  1342.764020  \n",
       "...          ...          ...  \n",
       "1746  110.402345  1552.190592  \n",
       "1747  132.976823  2241.921425  \n",
       "1748  116.333114  1468.777349  \n",
       "1749  100.408598  1854.712685  \n",
       "1750  138.795502  2335.231725  \n",
       "\n",
       "[1751 rows x 19957 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "merged_df = pd.merge(reference_csv, sample_csv, how='inner', left_on='Sample name', right_index=True)\n",
    "merged_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "merged_df.to_pickle(\"./datasets/GSE162330.pkl\")"
   ]
  }
 ],
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