feature_selection_without_variance.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "d526065f",
   "metadata": {},
   "source": [
    "# Feature selection without variance"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "342beaa6",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import statistics\n",
    "import seaborn as sns\n",
    "import matplotlib.pyplot as plt\n",
    "from scipy.stats import f_oneway, rankdata\n",
    "from sklearn.feature_selection import RFE\n",
    "from sklearn.feature_selection import mutual_info_classif\n",
    "from sklearn.linear_model import LinearRegression\n",
    "from imblearn.over_sampling import SMOTE"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b4fae360",
   "metadata": {},
   "source": [
    "## read in data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "242e963d",
   "metadata": {},
   "outputs": [],
   "source": [
    "# read in file\n",
    "df = pd.read_csv(\"Brain_GSE50161.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "c6eaa5fe",
   "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>samples</th>\n",
       "      <th>type</th>\n",
       "      <th>1007_s_at</th>\n",
       "      <th>1053_at</th>\n",
       "      <th>117_at</th>\n",
       "      <th>121_at</th>\n",
       "      <th>1255_g_at</th>\n",
       "      <th>1294_at</th>\n",
       "      <th>1316_at</th>\n",
       "      <th>1320_at</th>\n",
       "      <th>...</th>\n",
       "      <th>AFFX-r2-Ec-bioD-3_at</th>\n",
       "      <th>AFFX-r2-Ec-bioD-5_at</th>\n",
       "      <th>AFFX-r2-P1-cre-3_at</th>\n",
       "      <th>AFFX-r2-P1-cre-5_at</th>\n",
       "      <th>AFFX-ThrX-3_at</th>\n",
       "      <th>AFFX-ThrX-5_at</th>\n",
       "      <th>AFFX-ThrX-M_at</th>\n",
       "      <th>AFFX-TrpnX-3_at</th>\n",
       "      <th>AFFX-TrpnX-5_at</th>\n",
       "      <th>AFFX-TrpnX-M_at</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>834</td>\n",
       "      <td>ependymoma</td>\n",
       "      <td>12.498150</td>\n",
       "      <td>7.604868</td>\n",
       "      <td>6.880934</td>\n",
       "      <td>9.027128</td>\n",
       "      <td>4.176175</td>\n",
       "      <td>7.224920</td>\n",
       "      <td>6.085942</td>\n",
       "      <td>6.835999</td>\n",
       "      <td>...</td>\n",
       "      <td>9.979005</td>\n",
       "      <td>9.926470</td>\n",
       "      <td>12.719785</td>\n",
       "      <td>12.777792</td>\n",
       "      <td>5.403657</td>\n",
       "      <td>4.870548</td>\n",
       "      <td>4.047380</td>\n",
       "      <td>3.721936</td>\n",
       "      <td>4.516434</td>\n",
       "      <td>4.749940</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>835</td>\n",
       "      <td>ependymoma</td>\n",
       "      <td>13.067436</td>\n",
       "      <td>7.998090</td>\n",
       "      <td>7.209076</td>\n",
       "      <td>9.723322</td>\n",
       "      <td>4.826126</td>\n",
       "      <td>7.539381</td>\n",
       "      <td>6.250962</td>\n",
       "      <td>8.012549</td>\n",
       "      <td>...</td>\n",
       "      <td>11.924749</td>\n",
       "      <td>11.215930</td>\n",
       "      <td>13.605662</td>\n",
       "      <td>13.401342</td>\n",
       "      <td>5.224555</td>\n",
       "      <td>4.895315</td>\n",
       "      <td>3.786437</td>\n",
       "      <td>3.564481</td>\n",
       "      <td>4.430891</td>\n",
       "      <td>4.491416</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>836</td>\n",
       "      <td>ependymoma</td>\n",
       "      <td>13.068179</td>\n",
       "      <td>8.573674</td>\n",
       "      <td>8.647684</td>\n",
       "      <td>9.613002</td>\n",
       "      <td>4.396581</td>\n",
       "      <td>7.813101</td>\n",
       "      <td>6.007746</td>\n",
       "      <td>7.178156</td>\n",
       "      <td>...</td>\n",
       "      <td>12.154405</td>\n",
       "      <td>11.532460</td>\n",
       "      <td>13.764593</td>\n",
       "      <td>13.477800</td>\n",
       "      <td>5.303565</td>\n",
       "      <td>5.052184</td>\n",
       "      <td>4.005343</td>\n",
       "      <td>3.595382</td>\n",
       "      <td>4.563494</td>\n",
       "      <td>4.668827</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>837</td>\n",
       "      <td>ependymoma</td>\n",
       "      <td>12.456040</td>\n",
       "      <td>9.098977</td>\n",
       "      <td>6.628784</td>\n",
       "      <td>8.517677</td>\n",
       "      <td>4.154847</td>\n",
       "      <td>8.361843</td>\n",
       "      <td>6.596064</td>\n",
       "      <td>6.347285</td>\n",
       "      <td>...</td>\n",
       "      <td>11.969072</td>\n",
       "      <td>11.288801</td>\n",
       "      <td>13.600828</td>\n",
       "      <td>13.379029</td>\n",
       "      <td>4.953429</td>\n",
       "      <td>4.708371</td>\n",
       "      <td>3.892318</td>\n",
       "      <td>3.759429</td>\n",
       "      <td>4.748381</td>\n",
       "      <td>4.521275</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>838</td>\n",
       "      <td>ependymoma</td>\n",
       "      <td>12.699958</td>\n",
       "      <td>8.800721</td>\n",
       "      <td>11.556188</td>\n",
       "      <td>9.166309</td>\n",
       "      <td>4.165891</td>\n",
       "      <td>7.923826</td>\n",
       "      <td>6.212754</td>\n",
       "      <td>6.866387</td>\n",
       "      <td>...</td>\n",
       "      <td>11.411701</td>\n",
       "      <td>11.169317</td>\n",
       "      <td>13.751442</td>\n",
       "      <td>13.803646</td>\n",
       "      <td>4.892677</td>\n",
       "      <td>4.773806</td>\n",
       "      <td>3.796856</td>\n",
       "      <td>3.577544</td>\n",
       "      <td>4.504385</td>\n",
       "      <td>4.541450</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>125</th>\n",
       "      <td>959</td>\n",
       "      <td>pilocytic_astrocytoma</td>\n",
       "      <td>12.658228</td>\n",
       "      <td>8.843270</td>\n",
       "      <td>7.672655</td>\n",
       "      <td>9.125912</td>\n",
       "      <td>5.495477</td>\n",
       "      <td>8.603892</td>\n",
       "      <td>7.747514</td>\n",
       "      <td>5.828978</td>\n",
       "      <td>...</td>\n",
       "      <td>13.170441</td>\n",
       "      <td>12.676080</td>\n",
       "      <td>14.124837</td>\n",
       "      <td>13.996436</td>\n",
       "      <td>4.913579</td>\n",
       "      <td>4.399176</td>\n",
       "      <td>3.878855</td>\n",
       "      <td>3.680103</td>\n",
       "      <td>4.726784</td>\n",
       "      <td>4.564637</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>126</th>\n",
       "      <td>960</td>\n",
       "      <td>pilocytic_astrocytoma</td>\n",
       "      <td>12.812823</td>\n",
       "      <td>8.510550</td>\n",
       "      <td>8.729699</td>\n",
       "      <td>9.104402</td>\n",
       "      <td>3.967228</td>\n",
       "      <td>7.719089</td>\n",
       "      <td>7.092496</td>\n",
       "      <td>6.504812</td>\n",
       "      <td>...</td>\n",
       "      <td>13.040267</td>\n",
       "      <td>12.403316</td>\n",
       "      <td>13.978009</td>\n",
       "      <td>13.812916</td>\n",
       "      <td>5.189600</td>\n",
       "      <td>4.912618</td>\n",
       "      <td>3.764800</td>\n",
       "      <td>3.664920</td>\n",
       "      <td>4.628355</td>\n",
       "      <td>4.761351</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>127</th>\n",
       "      <td>961</td>\n",
       "      <td>pilocytic_astrocytoma</td>\n",
       "      <td>12.706991</td>\n",
       "      <td>8.795721</td>\n",
       "      <td>7.772359</td>\n",
       "      <td>8.327273</td>\n",
       "      <td>6.329383</td>\n",
       "      <td>8.550471</td>\n",
       "      <td>6.613332</td>\n",
       "      <td>6.308945</td>\n",
       "      <td>...</td>\n",
       "      <td>12.825383</td>\n",
       "      <td>12.439265</td>\n",
       "      <td>14.328373</td>\n",
       "      <td>14.008693</td>\n",
       "      <td>4.931460</td>\n",
       "      <td>4.712895</td>\n",
       "      <td>3.913637</td>\n",
       "      <td>3.700964</td>\n",
       "      <td>4.764693</td>\n",
       "      <td>4.834952</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>128</th>\n",
       "      <td>962</td>\n",
       "      <td>pilocytic_astrocytoma</td>\n",
       "      <td>12.684593</td>\n",
       "      <td>8.293938</td>\n",
       "      <td>7.228186</td>\n",
       "      <td>8.494428</td>\n",
       "      <td>6.049414</td>\n",
       "      <td>8.214729</td>\n",
       "      <td>7.287758</td>\n",
       "      <td>5.732710</td>\n",
       "      <td>...</td>\n",
       "      <td>13.116581</td>\n",
       "      <td>12.657967</td>\n",
       "      <td>14.390346</td>\n",
       "      <td>14.194904</td>\n",
       "      <td>4.871092</td>\n",
       "      <td>4.739400</td>\n",
       "      <td>3.782980</td>\n",
       "      <td>3.920363</td>\n",
       "      <td>4.665584</td>\n",
       "      <td>4.613326</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>129</th>\n",
       "      <td>963</td>\n",
       "      <td>pilocytic_astrocytoma</td>\n",
       "      <td>12.397722</td>\n",
       "      <td>8.843524</td>\n",
       "      <td>8.825100</td>\n",
       "      <td>8.551541</td>\n",
       "      <td>5.002072</td>\n",
       "      <td>8.547894</td>\n",
       "      <td>6.920827</td>\n",
       "      <td>5.738159</td>\n",
       "      <td>...</td>\n",
       "      <td>13.117180</td>\n",
       "      <td>12.699932</td>\n",
       "      <td>14.286779</td>\n",
       "      <td>14.088950</td>\n",
       "      <td>4.932377</td>\n",
       "      <td>4.700205</td>\n",
       "      <td>3.952850</td>\n",
       "      <td>3.678112</td>\n",
       "      <td>5.018501</td>\n",
       "      <td>4.704779</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>130 rows × 54677 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     samples                   type  1007_s_at   1053_at     117_at    121_at  \\\n",
       "0        834             ependymoma  12.498150  7.604868   6.880934  9.027128   \n",
       "1        835             ependymoma  13.067436  7.998090   7.209076  9.723322   \n",
       "2        836             ependymoma  13.068179  8.573674   8.647684  9.613002   \n",
       "3        837             ependymoma  12.456040  9.098977   6.628784  8.517677   \n",
       "4        838             ependymoma  12.699958  8.800721  11.556188  9.166309   \n",
       "..       ...                    ...        ...       ...        ...       ...   \n",
       "125      959  pilocytic_astrocytoma  12.658228  8.843270   7.672655  9.125912   \n",
       "126      960  pilocytic_astrocytoma  12.812823  8.510550   8.729699  9.104402   \n",
       "127      961  pilocytic_astrocytoma  12.706991  8.795721   7.772359  8.327273   \n",
       "128      962  pilocytic_astrocytoma  12.684593  8.293938   7.228186  8.494428   \n",
       "129      963  pilocytic_astrocytoma  12.397722  8.843524   8.825100  8.551541   \n",
       "\n",
       "     1255_g_at   1294_at   1316_at   1320_at  ...  AFFX-r2-Ec-bioD-3_at  \\\n",
       "0     4.176175  7.224920  6.085942  6.835999  ...              9.979005   \n",
       "1     4.826126  7.539381  6.250962  8.012549  ...             11.924749   \n",
       "2     4.396581  7.813101  6.007746  7.178156  ...             12.154405   \n",
       "3     4.154847  8.361843  6.596064  6.347285  ...             11.969072   \n",
       "4     4.165891  7.923826  6.212754  6.866387  ...             11.411701   \n",
       "..         ...       ...       ...       ...  ...                   ...   \n",
       "125   5.495477  8.603892  7.747514  5.828978  ...             13.170441   \n",
       "126   3.967228  7.719089  7.092496  6.504812  ...             13.040267   \n",
       "127   6.329383  8.550471  6.613332  6.308945  ...             12.825383   \n",
       "128   6.049414  8.214729  7.287758  5.732710  ...             13.116581   \n",
       "129   5.002072  8.547894  6.920827  5.738159  ...             13.117180   \n",
       "\n",
       "     AFFX-r2-Ec-bioD-5_at  AFFX-r2-P1-cre-3_at  AFFX-r2-P1-cre-5_at  \\\n",
       "0                9.926470            12.719785            12.777792   \n",
       "1               11.215930            13.605662            13.401342   \n",
       "2               11.532460            13.764593            13.477800   \n",
       "3               11.288801            13.600828            13.379029   \n",
       "4               11.169317            13.751442            13.803646   \n",
       "..                    ...                  ...                  ...   \n",
       "125             12.676080            14.124837            13.996436   \n",
       "126             12.403316            13.978009            13.812916   \n",
       "127             12.439265            14.328373            14.008693   \n",
       "128             12.657967            14.390346            14.194904   \n",
       "129             12.699932            14.286779            14.088950   \n",
       "\n",
       "     AFFX-ThrX-3_at  AFFX-ThrX-5_at  AFFX-ThrX-M_at  AFFX-TrpnX-3_at  \\\n",
       "0          5.403657        4.870548        4.047380         3.721936   \n",
       "1          5.224555        4.895315        3.786437         3.564481   \n",
       "2          5.303565        5.052184        4.005343         3.595382   \n",
       "3          4.953429        4.708371        3.892318         3.759429   \n",
       "4          4.892677        4.773806        3.796856         3.577544   \n",
       "..              ...             ...             ...              ...   \n",
       "125        4.913579        4.399176        3.878855         3.680103   \n",
       "126        5.189600        4.912618        3.764800         3.664920   \n",
       "127        4.931460        4.712895        3.913637         3.700964   \n",
       "128        4.871092        4.739400        3.782980         3.920363   \n",
       "129        4.932377        4.700205        3.952850         3.678112   \n",
       "\n",
       "     AFFX-TrpnX-5_at  AFFX-TrpnX-M_at  \n",
       "0           4.516434         4.749940  \n",
       "1           4.430891         4.491416  \n",
       "2           4.563494         4.668827  \n",
       "3           4.748381         4.521275  \n",
       "4           4.504385         4.541450  \n",
       "..               ...              ...  \n",
       "125         4.726784         4.564637  \n",
       "126         4.628355         4.761351  \n",
       "127         4.764693         4.834952  \n",
       "128         4.665584         4.613326  \n",
       "129         5.018501         4.704779  \n",
       "\n",
       "[130 rows x 54677 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "761c553b",
   "metadata": {},
   "outputs": [],
   "source": [
    "#Count the number of samples of five subtypes.\n",
    "def count_plot(label, title):\n",
    "    ax = sns.countplot(x=label)\n",
    "    for p in ax.patches:\n",
    "       ax.annotate('{:.1f}'.format(p.get_height()), (p.get_x()+0.25, p.get_height()+0.01))\n",
    "    plt.title(title)\n",
    "    plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "2d7e5b50",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "subtype_counts = count_plot(df[\"type\"], \"Five different subtype data counts\")\n",
    "subtype_counts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "c302ce7e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ependymoma               46\n",
      "glioblastoma             34\n",
      "medulloblastoma          22\n",
      "pilocytic_astrocytoma    15\n",
      "normal                   13\n",
      "Name: type, dtype: int64\n"
     ]
    }
   ],
   "source": [
    "# first column is the samples\n",
    "# second column is the types for brain cancers.\n",
    "print(df['type'].value_counts())\n",
    "# replace type to numbers\n",
    "df['type'] = df['type'].replace(['ependymoma', 'glioblastoma','medulloblastoma', 'pilocytic_astrocytoma','normal'],[0,1,2,3,4])"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "20758745",
   "metadata": {},
   "source": [
    "## Filter Methods"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "0aa69562",
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1000\n",
      "2000\n",
      "3000\n",
      "4000\n",
      "5000\n",
      "6000\n",
      "7000\n",
      "8000\n",
      "9000\n",
      "10000\n",
      "11000\n",
      "12000\n",
      "13000\n",
      "14000\n",
      "15000\n",
      "16000\n",
      "17000\n",
      "18000\n",
      "19000\n",
      "20000\n",
      "21000\n",
      "22000\n",
      "23000\n",
      "24000\n",
      "25000\n",
      "26000\n",
      "27000\n",
      "28000\n",
      "29000\n",
      "30000\n",
      "31000\n",
      "32000\n",
      "33000\n",
      "34000\n",
      "35000\n",
      "36000\n",
      "37000\n",
      "38000\n",
      "39000\n",
      "40000\n",
      "41000\n",
      "42000\n",
      "43000\n",
      "44000\n",
      "45000\n",
      "46000\n",
      "47000\n",
      "48000\n",
      "49000\n",
      "50000\n",
      "51000\n",
      "52000\n",
      "53000\n",
      "54000\n"
     ]
    }
   ],
   "source": [
    "# Use ANOVA to filter genes based on p-value\n",
    "\n",
    "stat_ANOVA = []\n",
    "\n",
    "# loop through each gene \n",
    "# to get gene expression values for a certain gene for each subtype\n",
    "# to get all gene expression values for each subtype (whole loop)\n",
    "for g in range(2, df.shape[1]):\n",
    "    \n",
    "    # subset type 0 (ependymoma) for gene g\n",
    "    # .iloc[:,g] means all rows and column g\n",
    "    type0 = np.array(df[df.type == 0].iloc[:,g])\n",
    "    \n",
    "    # subset type 1 (glioblastoma) for gene g\n",
    "    type1 = np.array(df[df.type == 1].iloc[:,g])\n",
    "    \n",
    "    # subset type 2 (medulloblastoma) for gene g\n",
    "    type2 = np.array(df[df.type == 2].iloc[:,g])\n",
    "    \n",
    "    # subset type 3 (pilocytic_astrocytoma) for gene g\n",
    "    type3 = np.array(df[df.type == 3].iloc[:,g])\n",
    "    \n",
    "    # subset type 4 (normal) for gene g\n",
    "    type4 = np.array(df[df.type == 4].iloc[:,g])\n",
    "    \n",
    "    # run 1-way between subjects ANOVA\n",
    "    # Returns: The computed F statistic of the test; The associated p-value from the F distribution.\n",
    "    result = f_oneway(type0, type1, type2, type3, type4)\n",
    "    \n",
    "    # append p-value\n",
    "    stat_ANOVA.append(result[1])\n",
    "        \n",
    "    if g%1000 == 0:\n",
    "        print(g)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "639456a6",
   "metadata": {},
   "outputs": [],
   "source": [
    "# if the p value of the specific gene (between all subtypes) is less than 0.0001 then return the gene\n",
    "# first two colunms are sample and type\n",
    "stat_TF = [True, True]\n",
    "\n",
    "for i in stat_ANOVA:\n",
    "    if i <= 0.0001:\n",
    "        stat_TF.append(True)\n",
    "    else:\n",
    "        stat_TF.append(False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "f0926a0f",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>samples</th>\n",
       "      <th>type</th>\n",
       "      <th>1007_s_at</th>\n",
       "      <th>1053_at</th>\n",
       "      <th>117_at</th>\n",
       "      <th>1255_g_at</th>\n",
       "      <th>1294_at</th>\n",
       "      <th>1431_at</th>\n",
       "      <th>1438_at</th>\n",
       "      <th>1487_at</th>\n",
       "      <th>...</th>\n",
       "      <th>91920_at</th>\n",
       "      <th>AFFX-HSAC07/X00351_3_at</th>\n",
       "      <th>AFFX-HSAC07/X00351_5_at</th>\n",
       "      <th>AFFX-HSAC07/X00351_M_at</th>\n",
       "      <th>AFFX-HUMGAPDH/M33197_3_at</th>\n",
       "      <th>AFFX-HUMGAPDH/M33197_M_at</th>\n",
       "      <th>AFFX-HUMISGF3A/M97935_3_at</th>\n",
       "      <th>AFFX-HUMISGF3A/M97935_MB_at</th>\n",
       "      <th>AFFX-PheX-M_at</th>\n",
       "      <th>AFFX-r2-Bs-phe-M_at</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>834</td>\n",
       "      <td>0</td>\n",
       "      <td>12.498150</td>\n",
       "      <td>7.604868</td>\n",
       "      <td>6.880934</td>\n",
       "      <td>4.176175</td>\n",
       "      <td>7.224920</td>\n",
       "      <td>5.513410</td>\n",
       "      <td>7.541986</td>\n",
       "      <td>7.905140</td>\n",
       "      <td>...</td>\n",
       "      <td>10.956206</td>\n",
       "      <td>13.087353</td>\n",
       "      <td>12.786701</td>\n",
       "      <td>13.104597</td>\n",
       "      <td>13.027510</td>\n",
       "      <td>13.092592</td>\n",
       "      <td>9.104209</td>\n",
       "      <td>7.452986</td>\n",
       "      <td>3.882678</td>\n",
       "      <td>4.483687</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>835</td>\n",
       "      <td>0</td>\n",
       "      <td>13.067436</td>\n",
       "      <td>7.998090</td>\n",
       "      <td>7.209076</td>\n",
       "      <td>4.826126</td>\n",
       "      <td>7.539381</td>\n",
       "      <td>6.173106</td>\n",
       "      <td>8.317030</td>\n",
       "      <td>8.269136</td>\n",
       "      <td>...</td>\n",
       "      <td>10.255266</td>\n",
       "      <td>13.912946</td>\n",
       "      <td>13.532344</td>\n",
       "      <td>13.814658</td>\n",
       "      <td>14.237459</td>\n",
       "      <td>14.229670</td>\n",
       "      <td>10.411498</td>\n",
       "      <td>9.122687</td>\n",
       "      <td>3.744942</td>\n",
       "      <td>3.673009</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>836</td>\n",
       "      <td>0</td>\n",
       "      <td>13.068179</td>\n",
       "      <td>8.573674</td>\n",
       "      <td>8.647684</td>\n",
       "      <td>4.396581</td>\n",
       "      <td>7.813101</td>\n",
       "      <td>6.323471</td>\n",
       "      <td>7.661874</td>\n",
       "      <td>8.327897</td>\n",
       "      <td>...</td>\n",
       "      <td>10.364209</td>\n",
       "      <td>14.378190</td>\n",
       "      <td>13.937428</td>\n",
       "      <td>14.248673</td>\n",
       "      <td>14.402930</td>\n",
       "      <td>14.447217</td>\n",
       "      <td>11.321259</td>\n",
       "      <td>9.822739</td>\n",
       "      <td>3.813011</td>\n",
       "      <td>3.541582</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>837</td>\n",
       "      <td>0</td>\n",
       "      <td>12.456040</td>\n",
       "      <td>9.098977</td>\n",
       "      <td>6.628784</td>\n",
       "      <td>4.154847</td>\n",
       "      <td>8.361843</td>\n",
       "      <td>6.008684</td>\n",
       "      <td>7.663790</td>\n",
       "      <td>7.730238</td>\n",
       "      <td>...</td>\n",
       "      <td>8.451971</td>\n",
       "      <td>13.755865</td>\n",
       "      <td>13.383430</td>\n",
       "      <td>13.660059</td>\n",
       "      <td>13.369370</td>\n",
       "      <td>13.457756</td>\n",
       "      <td>9.924395</td>\n",
       "      <td>8.028984</td>\n",
       "      <td>3.820466</td>\n",
       "      <td>3.593411</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>838</td>\n",
       "      <td>0</td>\n",
       "      <td>12.699958</td>\n",
       "      <td>8.800721</td>\n",
       "      <td>11.556188</td>\n",
       "      <td>4.165891</td>\n",
       "      <td>7.923826</td>\n",
       "      <td>5.279579</td>\n",
       "      <td>9.521956</td>\n",
       "      <td>7.581397</td>\n",
       "      <td>...</td>\n",
       "      <td>10.490535</td>\n",
       "      <td>14.077636</td>\n",
       "      <td>13.760155</td>\n",
       "      <td>14.042310</td>\n",
       "      <td>13.835195</td>\n",
       "      <td>14.029920</td>\n",
       "      <td>10.786574</td>\n",
       "      <td>9.086955</td>\n",
       "      <td>3.865816</td>\n",
       "      <td>4.355079</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>125</th>\n",
       "      <td>959</td>\n",
       "      <td>3</td>\n",
       "      <td>12.658228</td>\n",
       "      <td>8.843270</td>\n",
       "      <td>7.672655</td>\n",
       "      <td>5.495477</td>\n",
       "      <td>8.603892</td>\n",
       "      <td>4.967369</td>\n",
       "      <td>7.014209</td>\n",
       "      <td>8.666578</td>\n",
       "      <td>...</td>\n",
       "      <td>8.719159</td>\n",
       "      <td>13.967509</td>\n",
       "      <td>13.242701</td>\n",
       "      <td>13.713351</td>\n",
       "      <td>13.663155</td>\n",
       "      <td>13.609845</td>\n",
       "      <td>10.719271</td>\n",
       "      <td>8.359550</td>\n",
       "      <td>3.906140</td>\n",
       "      <td>3.892008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>126</th>\n",
       "      <td>960</td>\n",
       "      <td>3</td>\n",
       "      <td>12.812823</td>\n",
       "      <td>8.510550</td>\n",
       "      <td>8.729699</td>\n",
       "      <td>3.967228</td>\n",
       "      <td>7.719089</td>\n",
       "      <td>5.082896</td>\n",
       "      <td>7.981177</td>\n",
       "      <td>8.737005</td>\n",
       "      <td>...</td>\n",
       "      <td>9.022079</td>\n",
       "      <td>13.896949</td>\n",
       "      <td>13.232039</td>\n",
       "      <td>13.696252</td>\n",
       "      <td>14.382744</td>\n",
       "      <td>14.382647</td>\n",
       "      <td>10.303234</td>\n",
       "      <td>8.257289</td>\n",
       "      <td>4.002341</td>\n",
       "      <td>4.069697</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>127</th>\n",
       "      <td>961</td>\n",
       "      <td>3</td>\n",
       "      <td>12.706991</td>\n",
       "      <td>8.795721</td>\n",
       "      <td>7.772359</td>\n",
       "      <td>6.329383</td>\n",
       "      <td>8.550471</td>\n",
       "      <td>4.919414</td>\n",
       "      <td>6.638493</td>\n",
       "      <td>8.724114</td>\n",
       "      <td>...</td>\n",
       "      <td>9.545324</td>\n",
       "      <td>13.823257</td>\n",
       "      <td>12.218713</td>\n",
       "      <td>13.097621</td>\n",
       "      <td>13.699895</td>\n",
       "      <td>13.556569</td>\n",
       "      <td>11.074307</td>\n",
       "      <td>8.822692</td>\n",
       "      <td>3.904377</td>\n",
       "      <td>3.685399</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>128</th>\n",
       "      <td>962</td>\n",
       "      <td>3</td>\n",
       "      <td>12.684593</td>\n",
       "      <td>8.293938</td>\n",
       "      <td>7.228186</td>\n",
       "      <td>6.049414</td>\n",
       "      <td>8.214729</td>\n",
       "      <td>5.140635</td>\n",
       "      <td>7.225376</td>\n",
       "      <td>8.333919</td>\n",
       "      <td>...</td>\n",
       "      <td>10.455301</td>\n",
       "      <td>13.935221</td>\n",
       "      <td>13.133453</td>\n",
       "      <td>13.494138</td>\n",
       "      <td>13.499406</td>\n",
       "      <td>13.422512</td>\n",
       "      <td>10.848698</td>\n",
       "      <td>8.689571</td>\n",
       "      <td>3.809154</td>\n",
       "      <td>3.683920</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>129</th>\n",
       "      <td>963</td>\n",
       "      <td>3</td>\n",
       "      <td>12.397722</td>\n",
       "      <td>8.843524</td>\n",
       "      <td>8.825100</td>\n",
       "      <td>5.002072</td>\n",
       "      <td>8.547894</td>\n",
       "      <td>5.229208</td>\n",
       "      <td>6.839369</td>\n",
       "      <td>8.492447</td>\n",
       "      <td>...</td>\n",
       "      <td>8.478032</td>\n",
       "      <td>13.855325</td>\n",
       "      <td>13.000637</td>\n",
       "      <td>13.411613</td>\n",
       "      <td>13.939375</td>\n",
       "      <td>13.956265</td>\n",
       "      <td>10.665013</td>\n",
       "      <td>8.071967</td>\n",
       "      <td>3.797747</td>\n",
       "      <td>3.660039</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>130 rows × 21371 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     samples  type  1007_s_at   1053_at     117_at  1255_g_at   1294_at  \\\n",
       "0        834     0  12.498150  7.604868   6.880934   4.176175  7.224920   \n",
       "1        835     0  13.067436  7.998090   7.209076   4.826126  7.539381   \n",
       "2        836     0  13.068179  8.573674   8.647684   4.396581  7.813101   \n",
       "3        837     0  12.456040  9.098977   6.628784   4.154847  8.361843   \n",
       "4        838     0  12.699958  8.800721  11.556188   4.165891  7.923826   \n",
       "..       ...   ...        ...       ...        ...        ...       ...   \n",
       "125      959     3  12.658228  8.843270   7.672655   5.495477  8.603892   \n",
       "126      960     3  12.812823  8.510550   8.729699   3.967228  7.719089   \n",
       "127      961     3  12.706991  8.795721   7.772359   6.329383  8.550471   \n",
       "128      962     3  12.684593  8.293938   7.228186   6.049414  8.214729   \n",
       "129      963     3  12.397722  8.843524   8.825100   5.002072  8.547894   \n",
       "\n",
       "      1431_at   1438_at   1487_at  ...   91920_at  AFFX-HSAC07/X00351_3_at  \\\n",
       "0    5.513410  7.541986  7.905140  ...  10.956206                13.087353   \n",
       "1    6.173106  8.317030  8.269136  ...  10.255266                13.912946   \n",
       "2    6.323471  7.661874  8.327897  ...  10.364209                14.378190   \n",
       "3    6.008684  7.663790  7.730238  ...   8.451971                13.755865   \n",
       "4    5.279579  9.521956  7.581397  ...  10.490535                14.077636   \n",
       "..        ...       ...       ...  ...        ...                      ...   \n",
       "125  4.967369  7.014209  8.666578  ...   8.719159                13.967509   \n",
       "126  5.082896  7.981177  8.737005  ...   9.022079                13.896949   \n",
       "127  4.919414  6.638493  8.724114  ...   9.545324                13.823257   \n",
       "128  5.140635  7.225376  8.333919  ...  10.455301                13.935221   \n",
       "129  5.229208  6.839369  8.492447  ...   8.478032                13.855325   \n",
       "\n",
       "     AFFX-HSAC07/X00351_5_at  AFFX-HSAC07/X00351_M_at  \\\n",
       "0                  12.786701                13.104597   \n",
       "1                  13.532344                13.814658   \n",
       "2                  13.937428                14.248673   \n",
       "3                  13.383430                13.660059   \n",
       "4                  13.760155                14.042310   \n",
       "..                       ...                      ...   \n",
       "125                13.242701                13.713351   \n",
       "126                13.232039                13.696252   \n",
       "127                12.218713                13.097621   \n",
       "128                13.133453                13.494138   \n",
       "129                13.000637                13.411613   \n",
       "\n",
       "     AFFX-HUMGAPDH/M33197_3_at  AFFX-HUMGAPDH/M33197_M_at  \\\n",
       "0                    13.027510                  13.092592   \n",
       "1                    14.237459                  14.229670   \n",
       "2                    14.402930                  14.447217   \n",
       "3                    13.369370                  13.457756   \n",
       "4                    13.835195                  14.029920   \n",
       "..                         ...                        ...   \n",
       "125                  13.663155                  13.609845   \n",
       "126                  14.382744                  14.382647   \n",
       "127                  13.699895                  13.556569   \n",
       "128                  13.499406                  13.422512   \n",
       "129                  13.939375                  13.956265   \n",
       "\n",
       "     AFFX-HUMISGF3A/M97935_3_at  AFFX-HUMISGF3A/M97935_MB_at  AFFX-PheX-M_at  \\\n",
       "0                      9.104209                     7.452986        3.882678   \n",
       "1                     10.411498                     9.122687        3.744942   \n",
       "2                     11.321259                     9.822739        3.813011   \n",
       "3                      9.924395                     8.028984        3.820466   \n",
       "4                     10.786574                     9.086955        3.865816   \n",
       "..                          ...                          ...             ...   \n",
       "125                   10.719271                     8.359550        3.906140   \n",
       "126                   10.303234                     8.257289        4.002341   \n",
       "127                   11.074307                     8.822692        3.904377   \n",
       "128                   10.848698                     8.689571        3.809154   \n",
       "129                   10.665013                     8.071967        3.797747   \n",
       "\n",
       "     AFFX-r2-Bs-phe-M_at  \n",
       "0               4.483687  \n",
       "1               3.673009  \n",
       "2               3.541582  \n",
       "3               3.593411  \n",
       "4               4.355079  \n",
       "..                   ...  \n",
       "125             3.892008  \n",
       "126             4.069697  \n",
       "127             3.685399  \n",
       "128             3.683920  \n",
       "129             3.660039  \n",
       "\n",
       "[130 rows x 21371 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# stat_TF has the corresponding order with genes\n",
    "# if stat_TF = True, get the column through .loc\n",
    "df_ANOVA = df.loc[:,stat_TF]\n",
    "df_ANOVA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "18e8651e",
   "metadata": {},
   "outputs": [],
   "source": [
    "# We do not use variance to filter"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "52e5d6fb",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "IG done\n"
     ]
    }
   ],
   "source": [
    "# Use Information Gain to filter\n",
    "\n",
    "# x is columns for genes\n",
    "# y is the cancer type\n",
    "X = np.array(df_ANOVA.iloc[:,2:])\n",
    "y = np.array(df_ANOVA.iloc[:,1])\n",
    "\n",
    "IG = mutual_info_classif(X,y,n_neighbors = 5)\n",
    "print(\"IG done\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "c6af515c",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>samples</th>\n",
       "      <th>type</th>\n",
       "      <th>1438_at</th>\n",
       "      <th>1552258_at</th>\n",
       "      <th>1552286_at</th>\n",
       "      <th>1552293_at</th>\n",
       "      <th>1552309_a_at</th>\n",
       "      <th>1552347_at</th>\n",
       "      <th>1552436_a_at</th>\n",
       "      <th>1552487_a_at</th>\n",
       "      <th>...</th>\n",
       "      <th>51176_at</th>\n",
       "      <th>55093_at</th>\n",
       "      <th>57703_at</th>\n",
       "      <th>59999_at</th>\n",
       "      <th>63009_at</th>\n",
       "      <th>81811_at</th>\n",
       "      <th>AFFX-HSAC07/X00351_3_at</th>\n",
       "      <th>AFFX-HSAC07/X00351_5_at</th>\n",
       "      <th>AFFX-HSAC07/X00351_M_at</th>\n",
       "      <th>AFFX-r2-Bs-phe-M_at</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>834</td>\n",
       "      <td>0</td>\n",
       "      <td>7.541986</td>\n",
       "      <td>6.560058</td>\n",
       "      <td>6.889821</td>\n",
       "      <td>6.725073</td>\n",
       "      <td>6.998608</td>\n",
       "      <td>7.993485</td>\n",
       "      <td>5.793488</td>\n",
       "      <td>3.575070</td>\n",
       "      <td>...</td>\n",
       "      <td>8.845922</td>\n",
       "      <td>7.562261</td>\n",
       "      <td>5.200763</td>\n",
       "      <td>7.587168</td>\n",
       "      <td>7.785278</td>\n",
       "      <td>7.511650</td>\n",
       "      <td>13.087353</td>\n",
       "      <td>12.786701</td>\n",
       "      <td>13.104597</td>\n",
       "      <td>4.483687</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>835</td>\n",
       "      <td>0</td>\n",
       "      <td>8.317030</td>\n",
       "      <td>5.822008</td>\n",
       "      <td>7.413667</td>\n",
       "      <td>6.153470</td>\n",
       "      <td>5.850427</td>\n",
       "      <td>9.350866</td>\n",
       "      <td>5.258737</td>\n",
       "      <td>3.488097</td>\n",
       "      <td>...</td>\n",
       "      <td>8.702038</td>\n",
       "      <td>8.839196</td>\n",
       "      <td>5.488199</td>\n",
       "      <td>7.813305</td>\n",
       "      <td>7.143016</td>\n",
       "      <td>7.292757</td>\n",
       "      <td>13.912946</td>\n",
       "      <td>13.532344</td>\n",
       "      <td>13.814658</td>\n",
       "      <td>3.673009</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>836</td>\n",
       "      <td>0</td>\n",
       "      <td>7.661874</td>\n",
       "      <td>6.352456</td>\n",
       "      <td>7.032315</td>\n",
       "      <td>6.073385</td>\n",
       "      <td>7.742723</td>\n",
       "      <td>8.692528</td>\n",
       "      <td>6.162905</td>\n",
       "      <td>3.973754</td>\n",
       "      <td>...</td>\n",
       "      <td>9.273966</td>\n",
       "      <td>8.679280</td>\n",
       "      <td>5.718626</td>\n",
       "      <td>7.785056</td>\n",
       "      <td>7.555644</td>\n",
       "      <td>7.739923</td>\n",
       "      <td>14.378190</td>\n",
       "      <td>13.937428</td>\n",
       "      <td>14.248673</td>\n",
       "      <td>3.541582</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>837</td>\n",
       "      <td>0</td>\n",
       "      <td>7.663790</td>\n",
       "      <td>5.565398</td>\n",
       "      <td>7.732976</td>\n",
       "      <td>6.124541</td>\n",
       "      <td>7.417490</td>\n",
       "      <td>9.268702</td>\n",
       "      <td>5.438202</td>\n",
       "      <td>3.237992</td>\n",
       "      <td>...</td>\n",
       "      <td>9.882125</td>\n",
       "      <td>8.998287</td>\n",
       "      <td>6.501562</td>\n",
       "      <td>8.554817</td>\n",
       "      <td>8.272752</td>\n",
       "      <td>8.200230</td>\n",
       "      <td>13.755865</td>\n",
       "      <td>13.383430</td>\n",
       "      <td>13.660059</td>\n",
       "      <td>3.593411</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>838</td>\n",
       "      <td>0</td>\n",
       "      <td>9.521956</td>\n",
       "      <td>5.993222</td>\n",
       "      <td>7.253496</td>\n",
       "      <td>6.222004</td>\n",
       "      <td>7.179180</td>\n",
       "      <td>9.408418</td>\n",
       "      <td>6.417998</td>\n",
       "      <td>3.593244</td>\n",
       "      <td>...</td>\n",
       "      <td>8.934197</td>\n",
       "      <td>8.965294</td>\n",
       "      <td>6.551284</td>\n",
       "      <td>7.009931</td>\n",
       "      <td>7.232581</td>\n",
       "      <td>8.402796</td>\n",
       "      <td>14.077636</td>\n",
       "      <td>13.760155</td>\n",
       "      <td>14.042310</td>\n",
       "      <td>4.355079</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>125</th>\n",
       "      <td>959</td>\n",
       "      <td>3</td>\n",
       "      <td>7.014209</td>\n",
       "      <td>6.022244</td>\n",
       "      <td>6.603972</td>\n",
       "      <td>6.201650</td>\n",
       "      <td>7.299499</td>\n",
       "      <td>8.320582</td>\n",
       "      <td>5.256086</td>\n",
       "      <td>3.987297</td>\n",
       "      <td>...</td>\n",
       "      <td>9.905227</td>\n",
       "      <td>9.998747</td>\n",
       "      <td>6.201294</td>\n",
       "      <td>8.851932</td>\n",
       "      <td>7.585212</td>\n",
       "      <td>7.864563</td>\n",
       "      <td>13.967509</td>\n",
       "      <td>13.242701</td>\n",
       "      <td>13.713351</td>\n",
       "      <td>3.892008</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>126</th>\n",
       "      <td>960</td>\n",
       "      <td>3</td>\n",
       "      <td>7.981177</td>\n",
       "      <td>5.928188</td>\n",
       "      <td>6.595978</td>\n",
       "      <td>6.409211</td>\n",
       "      <td>7.388121</td>\n",
       "      <td>9.863542</td>\n",
       "      <td>6.366617</td>\n",
       "      <td>3.564149</td>\n",
       "      <td>...</td>\n",
       "      <td>9.624089</td>\n",
       "      <td>9.475274</td>\n",
       "      <td>6.392769</td>\n",
       "      <td>8.366345</td>\n",
       "      <td>7.664065</td>\n",
       "      <td>8.227930</td>\n",
       "      <td>13.896949</td>\n",
       "      <td>13.232039</td>\n",
       "      <td>13.696252</td>\n",
       "      <td>4.069697</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>127</th>\n",
       "      <td>961</td>\n",
       "      <td>3</td>\n",
       "      <td>6.638493</td>\n",
       "      <td>5.593812</td>\n",
       "      <td>6.815209</td>\n",
       "      <td>6.036911</td>\n",
       "      <td>7.548870</td>\n",
       "      <td>8.779005</td>\n",
       "      <td>5.136436</td>\n",
       "      <td>3.311504</td>\n",
       "      <td>...</td>\n",
       "      <td>9.743406</td>\n",
       "      <td>9.403521</td>\n",
       "      <td>6.963585</td>\n",
       "      <td>9.428674</td>\n",
       "      <td>7.457953</td>\n",
       "      <td>7.380839</td>\n",
       "      <td>13.823257</td>\n",
       "      <td>12.218713</td>\n",
       "      <td>13.097621</td>\n",
       "      <td>3.685399</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>128</th>\n",
       "      <td>962</td>\n",
       "      <td>3</td>\n",
       "      <td>7.225376</td>\n",
       "      <td>5.821805</td>\n",
       "      <td>6.823856</td>\n",
       "      <td>6.966092</td>\n",
       "      <td>7.800654</td>\n",
       "      <td>8.662069</td>\n",
       "      <td>5.391671</td>\n",
       "      <td>3.546279</td>\n",
       "      <td>...</td>\n",
       "      <td>9.848402</td>\n",
       "      <td>9.092632</td>\n",
       "      <td>6.476504</td>\n",
       "      <td>9.083276</td>\n",
       "      <td>7.170203</td>\n",
       "      <td>7.579404</td>\n",
       "      <td>13.935221</td>\n",
       "      <td>13.133453</td>\n",
       "      <td>13.494138</td>\n",
       "      <td>3.683920</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>129</th>\n",
       "      <td>963</td>\n",
       "      <td>3</td>\n",
       "      <td>6.839369</td>\n",
       "      <td>6.401216</td>\n",
       "      <td>6.109007</td>\n",
       "      <td>6.379778</td>\n",
       "      <td>7.318047</td>\n",
       "      <td>8.739987</td>\n",
       "      <td>5.401387</td>\n",
       "      <td>3.596227</td>\n",
       "      <td>...</td>\n",
       "      <td>9.612747</td>\n",
       "      <td>9.478974</td>\n",
       "      <td>6.217518</td>\n",
       "      <td>8.571241</td>\n",
       "      <td>7.207364</td>\n",
       "      <td>7.967292</td>\n",
       "      <td>13.855325</td>\n",
       "      <td>13.000637</td>\n",
       "      <td>13.411613</td>\n",
       "      <td>3.660039</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>130 rows × 3002 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     samples  type   1438_at  1552258_at  1552286_at  1552293_at  \\\n",
       "0        834     0  7.541986    6.560058    6.889821    6.725073   \n",
       "1        835     0  8.317030    5.822008    7.413667    6.153470   \n",
       "2        836     0  7.661874    6.352456    7.032315    6.073385   \n",
       "3        837     0  7.663790    5.565398    7.732976    6.124541   \n",
       "4        838     0  9.521956    5.993222    7.253496    6.222004   \n",
       "..       ...   ...       ...         ...         ...         ...   \n",
       "125      959     3  7.014209    6.022244    6.603972    6.201650   \n",
       "126      960     3  7.981177    5.928188    6.595978    6.409211   \n",
       "127      961     3  6.638493    5.593812    6.815209    6.036911   \n",
       "128      962     3  7.225376    5.821805    6.823856    6.966092   \n",
       "129      963     3  6.839369    6.401216    6.109007    6.379778   \n",
       "\n",
       "     1552309_a_at  1552347_at  1552436_a_at  1552487_a_at  ...  51176_at  \\\n",
       "0        6.998608    7.993485      5.793488      3.575070  ...  8.845922   \n",
       "1        5.850427    9.350866      5.258737      3.488097  ...  8.702038   \n",
       "2        7.742723    8.692528      6.162905      3.973754  ...  9.273966   \n",
       "3        7.417490    9.268702      5.438202      3.237992  ...  9.882125   \n",
       "4        7.179180    9.408418      6.417998      3.593244  ...  8.934197   \n",
       "..            ...         ...           ...           ...  ...       ...   \n",
       "125      7.299499    8.320582      5.256086      3.987297  ...  9.905227   \n",
       "126      7.388121    9.863542      6.366617      3.564149  ...  9.624089   \n",
       "127      7.548870    8.779005      5.136436      3.311504  ...  9.743406   \n",
       "128      7.800654    8.662069      5.391671      3.546279  ...  9.848402   \n",
       "129      7.318047    8.739987      5.401387      3.596227  ...  9.612747   \n",
       "\n",
       "     55093_at  57703_at  59999_at  63009_at  81811_at  \\\n",
       "0    7.562261  5.200763  7.587168  7.785278  7.511650   \n",
       "1    8.839196  5.488199  7.813305  7.143016  7.292757   \n",
       "2    8.679280  5.718626  7.785056  7.555644  7.739923   \n",
       "3    8.998287  6.501562  8.554817  8.272752  8.200230   \n",
       "4    8.965294  6.551284  7.009931  7.232581  8.402796   \n",
       "..        ...       ...       ...       ...       ...   \n",
       "125  9.998747  6.201294  8.851932  7.585212  7.864563   \n",
       "126  9.475274  6.392769  8.366345  7.664065  8.227930   \n",
       "127  9.403521  6.963585  9.428674  7.457953  7.380839   \n",
       "128  9.092632  6.476504  9.083276  7.170203  7.579404   \n",
       "129  9.478974  6.217518  8.571241  7.207364  7.967292   \n",
       "\n",
       "     AFFX-HSAC07/X00351_3_at  AFFX-HSAC07/X00351_5_at  \\\n",
       "0                  13.087353                12.786701   \n",
       "1                  13.912946                13.532344   \n",
       "2                  14.378190                13.937428   \n",
       "3                  13.755865                13.383430   \n",
       "4                  14.077636                13.760155   \n",
       "..                       ...                      ...   \n",
       "125                13.967509                13.242701   \n",
       "126                13.896949                13.232039   \n",
       "127                13.823257                12.218713   \n",
       "128                13.935221                13.133453   \n",
       "129                13.855325                13.000637   \n",
       "\n",
       "     AFFX-HSAC07/X00351_M_at  AFFX-r2-Bs-phe-M_at  \n",
       "0                  13.104597             4.483687  \n",
       "1                  13.814658             3.673009  \n",
       "2                  14.248673             3.541582  \n",
       "3                  13.660059             3.593411  \n",
       "4                  14.042310             4.355079  \n",
       "..                       ...                  ...  \n",
       "125                13.713351             3.892008  \n",
       "126                13.696252             4.069697  \n",
       "127                13.097621             3.685399  \n",
       "128                13.494138             3.683920  \n",
       "129                13.411613             3.660039  \n",
       "\n",
       "[130 rows x 3002 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Select top 3000 feature based on importance from Information Gain\n",
    "rank = rankdata(IG)\n",
    "rank_TF = [True, True]\n",
    "for i in rank:\n",
    "    if i <= 3000:\n",
    "        rank_TF.append(True)\n",
    "    else:\n",
    "        rank_TF.append(False)\n",
    "\n",
    "df_ig = df_ANOVA.loc[:,rank_TF]\n",
    "df_ig"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0f69f424",
   "metadata": {},
   "source": [
    "## Wrapper Methods"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "efb73e05",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "rfe done\n",
      "fit done\n"
     ]
    }
   ],
   "source": [
    "#x is columns for genes (features)\n",
    "#y is the cancer type\n",
    "X_new = df_ig.iloc[:,2:]\n",
    "y_new = df_ig.iloc[:,1]\n",
    "model = LinearRegression()\n",
    "rfe = RFE(model, n_features_to_select = 300)\n",
    "print(\"rfe done\")\n",
    "#Use RFE to select the top 300 features \n",
    "fit = rfe.fit(X_new, y_new)\n",
    "print('fit done')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "192dc28b",
   "metadata": {},
   "outputs": [],
   "source": [
    "RFE_results = []\n",
    "for i in range(X_new.shape[1]):\n",
    "    RFE_results.append(rfe.support_[i])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "ff08f125",
   "metadata": {},
   "outputs": [],
   "source": [
    "RFE_TF = [True, True]\n",
    "for i in RFE_results:\n",
    "    if i == True:\n",
    "        RFE_TF.append(True)\n",
    "    else:\n",
    "        RFE_TF.append(False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "891fc494",
   "metadata": {},
   "outputs": [],
   "source": [
    "df_RFE = df_ig.loc[:,RFE_TF]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "b9f5aa55",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<div>\n",
       "<style scoped>\n",
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       "      <th></th>\n",
       "      <th>type</th>\n",
       "      <th>1552309_a_at</th>\n",
       "      <th>1552760_at</th>\n",
       "      <th>1552904_at</th>\n",
       "      <th>1553335_x_at</th>\n",
       "      <th>1553872_at</th>\n",
       "      <th>1554501_at</th>\n",
       "      <th>1554507_at</th>\n",
       "      <th>1554544_a_at</th>\n",
       "      <th>1554773_at</th>\n",
       "      <th>...</th>\n",
       "      <th>244286_at</th>\n",
       "      <th>244327_at</th>\n",
       "      <th>244377_at</th>\n",
       "      <th>244420_at</th>\n",
       "      <th>244493_at</th>\n",
       "      <th>244751_at</th>\n",
       "      <th>244845_at</th>\n",
       "      <th>32088_at</th>\n",
       "      <th>39313_at</th>\n",
       "      <th>AFFX-HSAC07/X00351_5_at</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>6.998608</td>\n",
       "      <td>4.675092</td>\n",
       "      <td>3.106465</td>\n",
       "      <td>6.325314</td>\n",
       "      <td>6.304472</td>\n",
       "      <td>5.928285</td>\n",
       "      <td>4.015369</td>\n",
       "      <td>8.396550</td>\n",
       "      <td>5.989973</td>\n",
       "      <td>...</td>\n",
       "      <td>5.478364</td>\n",
       "      <td>5.201315</td>\n",
       "      <td>7.472457</td>\n",
       "      <td>6.846873</td>\n",
       "      <td>3.423704</td>\n",
       "      <td>6.001562</td>\n",
       "      <td>3.801157</td>\n",
       "      <td>3.942963</td>\n",
       "      <td>4.775633</td>\n",
       "      <td>12.786701</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0</td>\n",
       "      <td>5.850427</td>\n",
       "      <td>6.356873</td>\n",
       "      <td>3.156217</td>\n",
       "      <td>4.844061</td>\n",
       "      <td>6.416582</td>\n",
       "      <td>7.601599</td>\n",
       "      <td>3.204273</td>\n",
       "      <td>8.035201</td>\n",
       "      <td>6.604099</td>\n",
       "      <td>...</td>\n",
       "      <td>4.618364</td>\n",
       "      <td>4.602442</td>\n",
       "      <td>7.238519</td>\n",
       "      <td>7.487388</td>\n",
       "      <td>3.214800</td>\n",
       "      <td>5.518132</td>\n",
       "      <td>3.683462</td>\n",
       "      <td>5.714204</td>\n",
       "      <td>5.482738</td>\n",
       "      <td>13.532344</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0</td>\n",
       "      <td>7.742723</td>\n",
       "      <td>5.009840</td>\n",
       "      <td>3.184464</td>\n",
       "      <td>5.040621</td>\n",
       "      <td>6.434343</td>\n",
       "      <td>6.058108</td>\n",
       "      <td>4.369383</td>\n",
       "      <td>8.530794</td>\n",
       "      <td>7.024837</td>\n",
       "      <td>...</td>\n",
       "      <td>5.874003</td>\n",
       "      <td>4.648651</td>\n",
       "      <td>7.023025</td>\n",
       "      <td>6.587248</td>\n",
       "      <td>3.078852</td>\n",
       "      <td>5.927809</td>\n",
       "      <td>4.107657</td>\n",
       "      <td>4.990260</td>\n",
       "      <td>4.987844</td>\n",
       "      <td>13.937428</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0</td>\n",
       "      <td>7.417490</td>\n",
       "      <td>4.809402</td>\n",
       "      <td>3.467257</td>\n",
       "      <td>5.525078</td>\n",
       "      <td>6.745095</td>\n",
       "      <td>5.445093</td>\n",
       "      <td>3.394249</td>\n",
       "      <td>6.981226</td>\n",
       "      <td>6.222976</td>\n",
       "      <td>...</td>\n",
       "      <td>5.890145</td>\n",
       "      <td>4.343202</td>\n",
       "      <td>7.052640</td>\n",
       "      <td>6.236118</td>\n",
       "      <td>3.429725</td>\n",
       "      <td>5.952769</td>\n",
       "      <td>4.595754</td>\n",
       "      <td>5.184928</td>\n",
       "      <td>5.683947</td>\n",
       "      <td>13.383430</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0</td>\n",
       "      <td>7.179180</td>\n",
       "      <td>4.404772</td>\n",
       "      <td>3.205305</td>\n",
       "      <td>5.471905</td>\n",
       "      <td>6.799948</td>\n",
       "      <td>6.601058</td>\n",
       "      <td>4.431447</td>\n",
       "      <td>7.199892</td>\n",
       "      <td>6.217172</td>\n",
       "      <td>...</td>\n",
       "      <td>5.510016</td>\n",
       "      <td>4.523162</td>\n",
       "      <td>7.929837</td>\n",
       "      <td>7.671461</td>\n",
       "      <td>3.294988</td>\n",
       "      <td>5.653083</td>\n",
       "      <td>3.379933</td>\n",
       "      <td>4.888335</td>\n",
       "      <td>4.792557</td>\n",
       "      <td>13.760155</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>125</th>\n",
       "      <td>3</td>\n",
       "      <td>7.299499</td>\n",
       "      <td>4.751666</td>\n",
       "      <td>3.370705</td>\n",
       "      <td>5.334349</td>\n",
       "      <td>6.660259</td>\n",
       "      <td>6.838204</td>\n",
       "      <td>4.303145</td>\n",
       "      <td>8.041560</td>\n",
       "      <td>5.935573</td>\n",
       "      <td>...</td>\n",
       "      <td>5.990447</td>\n",
       "      <td>4.677889</td>\n",
       "      <td>7.393468</td>\n",
       "      <td>6.913413</td>\n",
       "      <td>3.184355</td>\n",
       "      <td>7.046908</td>\n",
       "      <td>5.840083</td>\n",
       "      <td>5.374284</td>\n",
       "      <td>7.177827</td>\n",
       "      <td>13.242701</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>126</th>\n",
       "      <td>3</td>\n",
       "      <td>7.388121</td>\n",
       "      <td>5.120510</td>\n",
       "      <td>3.413714</td>\n",
       "      <td>5.264219</td>\n",
       "      <td>6.976792</td>\n",
       "      <td>8.424854</td>\n",
       "      <td>3.438830</td>\n",
       "      <td>8.264806</td>\n",
       "      <td>6.180678</td>\n",
       "      <td>...</td>\n",
       "      <td>5.657150</td>\n",
       "      <td>5.630257</td>\n",
       "      <td>6.553336</td>\n",
       "      <td>6.118621</td>\n",
       "      <td>2.974504</td>\n",
       "      <td>6.664799</td>\n",
       "      <td>4.602616</td>\n",
       "      <td>4.995438</td>\n",
       "      <td>5.637364</td>\n",
       "      <td>13.232039</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>127</th>\n",
       "      <td>3</td>\n",
       "      <td>7.548870</td>\n",
       "      <td>7.366910</td>\n",
       "      <td>3.351634</td>\n",
       "      <td>5.436412</td>\n",
       "      <td>6.489141</td>\n",
       "      <td>6.329290</td>\n",
       "      <td>5.779441</td>\n",
       "      <td>8.114371</td>\n",
       "      <td>6.019242</td>\n",
       "      <td>...</td>\n",
       "      <td>5.268553</td>\n",
       "      <td>5.213805</td>\n",
       "      <td>7.442833</td>\n",
       "      <td>5.672894</td>\n",
       "      <td>3.190270</td>\n",
       "      <td>6.493181</td>\n",
       "      <td>4.403823</td>\n",
       "      <td>6.153474</td>\n",
       "      <td>6.136671</td>\n",
       "      <td>12.218713</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>128</th>\n",
       "      <td>3</td>\n",
       "      <td>7.800654</td>\n",
       "      <td>7.518995</td>\n",
       "      <td>3.495913</td>\n",
       "      <td>5.813444</td>\n",
       "      <td>6.643192</td>\n",
       "      <td>7.501441</td>\n",
       "      <td>7.847652</td>\n",
       "      <td>9.493311</td>\n",
       "      <td>6.398645</td>\n",
       "      <td>...</td>\n",
       "      <td>5.605629</td>\n",
       "      <td>4.950985</td>\n",
       "      <td>7.170843</td>\n",
       "      <td>6.847570</td>\n",
       "      <td>3.396742</td>\n",
       "      <td>6.473156</td>\n",
       "      <td>4.777800</td>\n",
       "      <td>5.188731</td>\n",
       "      <td>7.109605</td>\n",
       "      <td>13.133453</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>129</th>\n",
       "      <td>3</td>\n",
       "      <td>7.318047</td>\n",
       "      <td>5.671655</td>\n",
       "      <td>3.524098</td>\n",
       "      <td>5.800253</td>\n",
       "      <td>7.354228</td>\n",
       "      <td>7.150634</td>\n",
       "      <td>6.637282</td>\n",
       "      <td>8.415955</td>\n",
       "      <td>6.228810</td>\n",
       "      <td>...</td>\n",
       "      <td>5.842412</td>\n",
       "      <td>5.918461</td>\n",
       "      <td>7.549482</td>\n",
       "      <td>6.413308</td>\n",
       "      <td>2.993329</td>\n",
       "      <td>6.678276</td>\n",
       "      <td>4.923069</td>\n",
       "      <td>4.852181</td>\n",
       "      <td>7.280354</td>\n",
       "      <td>13.000637</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>130 rows × 301 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     type  1552309_a_at  1552760_at  1552904_at  1553335_x_at  1553872_at  \\\n",
       "0       0      6.998608    4.675092    3.106465      6.325314    6.304472   \n",
       "1       0      5.850427    6.356873    3.156217      4.844061    6.416582   \n",
       "2       0      7.742723    5.009840    3.184464      5.040621    6.434343   \n",
       "3       0      7.417490    4.809402    3.467257      5.525078    6.745095   \n",
       "4       0      7.179180    4.404772    3.205305      5.471905    6.799948   \n",
       "..    ...           ...         ...         ...           ...         ...   \n",
       "125     3      7.299499    4.751666    3.370705      5.334349    6.660259   \n",
       "126     3      7.388121    5.120510    3.413714      5.264219    6.976792   \n",
       "127     3      7.548870    7.366910    3.351634      5.436412    6.489141   \n",
       "128     3      7.800654    7.518995    3.495913      5.813444    6.643192   \n",
       "129     3      7.318047    5.671655    3.524098      5.800253    7.354228   \n",
       "\n",
       "     1554501_at  1554507_at  1554544_a_at  1554773_at  ...  244286_at  \\\n",
       "0      5.928285    4.015369      8.396550    5.989973  ...   5.478364   \n",
       "1      7.601599    3.204273      8.035201    6.604099  ...   4.618364   \n",
       "2      6.058108    4.369383      8.530794    7.024837  ...   5.874003   \n",
       "3      5.445093    3.394249      6.981226    6.222976  ...   5.890145   \n",
       "4      6.601058    4.431447      7.199892    6.217172  ...   5.510016   \n",
       "..          ...         ...           ...         ...  ...        ...   \n",
       "125    6.838204    4.303145      8.041560    5.935573  ...   5.990447   \n",
       "126    8.424854    3.438830      8.264806    6.180678  ...   5.657150   \n",
       "127    6.329290    5.779441      8.114371    6.019242  ...   5.268553   \n",
       "128    7.501441    7.847652      9.493311    6.398645  ...   5.605629   \n",
       "129    7.150634    6.637282      8.415955    6.228810  ...   5.842412   \n",
       "\n",
       "     244327_at  244377_at  244420_at  244493_at  244751_at  244845_at  \\\n",
       "0     5.201315   7.472457   6.846873   3.423704   6.001562   3.801157   \n",
       "1     4.602442   7.238519   7.487388   3.214800   5.518132   3.683462   \n",
       "2     4.648651   7.023025   6.587248   3.078852   5.927809   4.107657   \n",
       "3     4.343202   7.052640   6.236118   3.429725   5.952769   4.595754   \n",
       "4     4.523162   7.929837   7.671461   3.294988   5.653083   3.379933   \n",
       "..         ...        ...        ...        ...        ...        ...   \n",
       "125   4.677889   7.393468   6.913413   3.184355   7.046908   5.840083   \n",
       "126   5.630257   6.553336   6.118621   2.974504   6.664799   4.602616   \n",
       "127   5.213805   7.442833   5.672894   3.190270   6.493181   4.403823   \n",
       "128   4.950985   7.170843   6.847570   3.396742   6.473156   4.777800   \n",
       "129   5.918461   7.549482   6.413308   2.993329   6.678276   4.923069   \n",
       "\n",
       "     32088_at  39313_at  AFFX-HSAC07/X00351_5_at  \n",
       "0    3.942963  4.775633                12.786701  \n",
       "1    5.714204  5.482738                13.532344  \n",
       "2    4.990260  4.987844                13.937428  \n",
       "3    5.184928  5.683947                13.383430  \n",
       "4    4.888335  4.792557                13.760155  \n",
       "..        ...       ...                      ...  \n",
       "125  5.374284  7.177827                13.242701  \n",
       "126  4.995438  5.637364                13.232039  \n",
       "127  6.153474  6.136671                12.218713  \n",
       "128  5.188731  7.109605                13.133453  \n",
       "129  4.852181  7.280354                13.000637  \n",
       "\n",
       "[130 rows x 301 columns]"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_RFE.iloc[:,1:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "3e98f9aa",
   "metadata": {},
   "outputs": [],
   "source": [
    "# store the final dataset after the feature selection is done\n",
    "df_RFE.iloc[:,1:].to_csv(\"df_wo_var.csv\", index = False)"
   ]
  }
 ],
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