Untitled.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      " * Warning: The handling of integer data will change in version 0.22. Currently, the categories are determined based on the range [0, max(values)], while in the future they will be determined based on the unique values.\n",
      "If you want the future behaviour and silence this warning, you can specify \"categories='auto'\".\n",
      "In case you used a LabelEncoder before this OneHotEncoder to convert the categories to integers, then you can now use the OneHotEncoder directly.\n",
      " * Warning: Can't extract feature 'mad'.\n",
      " Exception message: AttributeError(\"module 'scipy.stats' has no attribute 'median_absolute_deviation'\").\n",
      " Will set it as 'np.nan' for all summary functions.\n",
      " * Warning: Mean of empty slice.\n",
      " * Warning: invalid value encountered in double_scalars\n",
      " * Warning: Can't summarize feature 'mad' with summary 'mean'. Will set it as 'np.nan'.\n",
      " * Warning: Can't summarize feature 'mad' with summary 'sd'. Will set it as 'np.nan'.\n",
      " * Warning: Can't extract feature 'leaves'.\n",
      " Exception message: AttributeError(\"'sklearn.tree._tree.Tree' object has no attribute 'n_leaves'\").\n",
      " * Warning: Can't extract feature 'leaves_homo'.\n",
      " Exception message: AttributeError(\"'sklearn.tree._tree.Tree' object has no attribute 'n_leaves'\").\n",
      " Will set it as 'np.nan' for all summary functions.\n",
      " * Warning: Can't summarize feature 'leaves_homo' with summary 'mean'. Will set it as 'np.nan'.\n",
      " * Warning: Can't summarize feature 'leaves_homo' with summary 'sd'. Will set it as 'np.nan'.\n",
      " * Warning: Can't extract feature 'leaves_per_class'.\n",
      " Exception message: AttributeError(\"'sklearn.tree._tree.Tree' object has no attribute 'n_leaves'\").\n",
      " Will set it as 'np.nan' for all summary functions.\n",
      " * Warning: Can't summarize feature 'leaves_per_class' with summary 'mean'. Will set it as 'np.nan'.\n",
      " * Warning: Can't summarize feature 'leaves_per_class' with summary 'sd'. Will set it as 'np.nan'.\n",
      " * Warning: Can't extract feature 'nodes'.\n",
      " Exception message: AttributeError(\"'sklearn.tree._tree.Tree' object has no attribute 'n_leaves'\").\n",
      " * Warning: Can't extract feature 'nodes_per_attr'.\n",
      " Exception message: AttributeError(\"'sklearn.tree._tree.Tree' object has no attribute 'n_leaves'\").\n",
      " * Warning: Can't extract feature 'nodes_per_inst'.\n",
      " Exception message: AttributeError(\"'sklearn.tree._tree.Tree' object has no attribute 'n_leaves'\").\n",
      " * Warning: The handling of integer data will change in version 0.22. Currently, the categories are determined based on the range [0, max(values)], while in the future they will be determined based on the unique values.\n",
      "If you want the future behaviour and silence this warning, you can specify \"categories='auto'\".\n",
      "In case you used a LabelEncoder before this OneHotEncoder to convert the categories to integers, then you can now use the OneHotEncoder directly.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(['attr_conc.mean', 'attr_conc.sd', 'attr_ent.mean', 'attr_ent.sd', 'attr_to_inst', 'best_node.mean', 'best_node.sd', 'can_cor.mean', 'can_cor.sd', 'cat_to_num', 'class_conc.mean', 'class_conc.sd', 'class_ent', 'cor.mean', 'cor.sd', 'cov.mean', 'cov.sd', 'eigenvalues.mean', 'eigenvalues.sd', 'elite_nn.mean', 'elite_nn.sd', 'eq_num_attr', 'freq_class.mean', 'freq_class.sd', 'g_mean.mean', 'g_mean.sd', 'gravity', 'h_mean.mean', 'h_mean.sd', 'inst_to_attr', 'iq_range.mean', 'iq_range.sd', 'joint_ent.mean', 'joint_ent.sd', 'kurtosis.mean', 'kurtosis.sd', 'leaves', 'leaves_branch.mean', 'leaves_branch.sd', 'leaves_corrob.mean', 'leaves_corrob.sd', 'leaves_homo.mean', 'leaves_homo.sd', 'leaves_per_class.mean', 'leaves_per_class.sd', 'lh_trace', 'linear_discr.mean', 'linear_discr.sd', 'mad.mean', 'mad.sd', 'max.mean', 'max.sd', 'mean.mean', 'mean.sd', 'median.mean', 'median.sd', 'min.mean', 'min.sd', 'mut_inf.mean', 'mut_inf.sd', 'naive_bayes.mean', 'naive_bayes.sd', 'nodes', 'nodes_per_attr', 'nodes_per_inst', 'nodes_per_level.mean', 'nodes_per_level.sd', 'nodes_repeated.mean', 'nodes_repeated.sd', 'nr_attr', 'nr_bin', 'nr_cat', 'nr_class', 'nr_cor_attr', 'nr_disc', 'nr_inst', 'nr_norm', 'nr_num', 'nr_outliers', 'ns_ratio', 'num_to_cat', 'one_nn.mean', 'one_nn.sd', 'p_trace', 'random_node.mean', 'random_node.sd', 'range.mean', 'range.sd', 'roy_root', 'sd.mean', 'sd.sd', 'sd_ratio', 'skewness.mean', 'skewness.sd', 'sparsity.mean', 'sparsity.sd', 't_mean.mean', 't_mean.sd', 'tree_depth.mean', 'tree_depth.sd', 'tree_imbalance.mean', 'tree_imbalance.sd', 'tree_shape.mean', 'tree_shape.sd', 'var.mean', 'var.sd', 'var_importance.mean', 'var_importance.sd', 'w_lambda', 'worst_node.mean', 'worst_node.sd'], [0.20980476831180148, 0.1195879817732128, 2.2771912775084115, 0.06103943244855649, 0.02666666666666667, 0.6666666666666667, 1.1702778228589004e-16, 0.7280089560229875, 0.3631869218945755, 0.0, 0.27347384133126745, 0.14091096327223987, 1.584962500721156, 0.594116025760156, 0.3375443182856702, 0.5966542132736764, 0.5582672431248461, 1.1432392617449667, 2.0587713015069755, 0.8866666666666667, 0.07730012058189371, 1.8780672345507194, 0.3333333333333333, 0.0, 3.2230731578977903, 2.0229431040263726, 3.2082811597489393, 2.9783891110628673, 2.145948231748242, 37.5, 1.7000000000000002, 1.2754084313139324, 3.0182209990602855, 0.3821875549207214, -0.8105361276250795, 0.7326910069728161, nan, 3.7777777777777777, 1.2018504251546631, 0.1111111111111111, 0.15051762539834182, nan, nan, nan, nan, 32.4773135181212, 0.9800000000000001, 0.04499657051403685, nan, nan, 5.425000000000001, 2.4431878083083722, 3.4645000000000006, 1.918485079431164, 3.6125000000000003, 1.919364043982624, 1.8499999999999999, 1.8083141320025125, 0.8439327791692818, 0.4222019352579773, 0.9533333333333334, 0.04499657051403685, nan, nan, nan, 1.6, 0.8944271909999159, 2.6666666666666665, 1.1547005383792515, 4, 0, 0, 3, 0.5, 2, 150, 1, 4, 1, 1.698308838945616, nan, 0.96, 0.05621826951410451, 1.1918988203346168, 0.6666666666666667, 1.1702778228589004e-16, 3.5750000000000006, 1.6500000000000001, 32.19192247318928, 0.9478670787835934, 0.5712994109375844, 1.2708666438750906, 0.06273198447775732, 0.29439896290757683, 0.0287147773948895, 0.011032357470087495, 3.4705555555555554, 1.9048021402275979, 3.0588235294117645, 1.4348601079588785, 0.19491705385114735, 0.13300709991513865, 0.2708333333333333, 0.10711960313126631, 1.1432392617449665, 1.3325463926454557, 0.25, 0.44888544020359966, 0.023438635357730147, 0.58, 0.07062332703142533])\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      " * Warning: Can't extract feature 'mad'.\n",
      " Exception message: AttributeError(\"module 'scipy.stats' has no attribute 'median_absolute_deviation'\").\n",
      " Will set it as 'np.nan' for all summary functions.\n",
      " * Warning: Mean of empty slice.\n",
      " * Warning: invalid value encountered in double_scalars\n",
      " * Warning: Can't summarize feature 'mad' with summary 'mean'. Will set it as 'np.nan'.\n",
      " * Warning: Can't summarize feature 'mad' with summary 'sd'. Will set it as 'np.nan'.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(['attr_conc.mean', 'attr_conc.sd', 'attr_ent.mean', 'attr_ent.sd', 'attr_to_inst', 'can_cor.mean', 'can_cor.sd', 'cat_to_num', 'class_conc.mean', 'class_conc.sd', 'class_ent', 'cor.mean', 'cor.sd', 'cov.mean', 'cov.sd', 'eigenvalues.mean', 'eigenvalues.sd', 'eq_num_attr', 'freq_class.mean', 'freq_class.sd', 'g_mean.mean', 'g_mean.sd', 'gravity', 'h_mean.mean', 'h_mean.sd', 'inst_to_attr', 'iq_range.mean', 'iq_range.sd', 'joint_ent.mean', 'joint_ent.sd', 'kurtosis.mean', 'kurtosis.sd', 'lh_trace', 'mad.mean', 'mad.sd', 'max.mean', 'max.sd', 'mean.mean', 'mean.sd', 'median.mean', 'median.sd', 'min.mean', 'min.sd', 'mut_inf.mean', 'mut_inf.sd', 'nr_attr', 'nr_bin', 'nr_cat', 'nr_class', 'nr_cor_attr', 'nr_disc', 'nr_inst', 'nr_norm', 'nr_num', 'nr_outliers', 'ns_ratio', 'num_to_cat', 'p_trace', 'range.mean', 'range.sd', 'roy_root', 'sd.mean', 'sd.sd', 'sd_ratio', 'skewness.mean', 'skewness.sd', 'sparsity.mean', 'sparsity.sd', 't_mean.mean', 't_mean.sd', 'var.mean', 'var.sd', 'w_lambda'], [0.20980476831180148, 0.1195879817732128, 2.2771912775084115, 0.06103943244855649, 0.02666666666666667, 0.7280089560229875, 0.3631869218945755, 0.0, 0.27347384133126745, 0.14091096327223987, 1.584962500721156, 0.594116025760156, 0.3375443182856702, 0.5966542132736764, 0.5582672431248461, 1.1432392617449667, 2.0587713015069755, 1.8780672345507194, 0.3333333333333333, 0.0, 3.2230731578977903, 2.0229431040263726, 3.2082811597489393, 2.9783891110628673, 2.145948231748242, 37.5, 1.7000000000000002, 1.2754084313139324, 3.0182209990602855, 0.3821875549207214, -0.8105361276250795, 0.7326910069728161, 32.4773135181212, nan, nan, 5.425000000000001, 2.4431878083083722, 3.4645000000000006, 1.918485079431164, 3.6125000000000003, 1.919364043982624, 1.8499999999999999, 1.8083141320025125, 0.8439327791692818, 0.4222019352579773, 4, 0, 0, 3, 0.5, 2, 150, 1, 4, 1, 1.698308838945616, nan, 1.1918988203346168, 3.5750000000000006, 1.6500000000000001, 32.19192247318928, 0.9478670787835934, 0.5712994109375844, 1.2708666438750906, 0.06273198447775732, 0.29439896290757683, 0.0287147773948895, 0.011032357470087495, 3.4705555555555554, 1.9048021402275979, 1.1432392617449665, 1.3325463926454557, 0.023438635357730147])\n"
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    {
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     "text": [
      " * Warning: The handling of integer data will change in version 0.22. Currently, the categories are determined based on the range [0, max(values)], while in the future they will be determined based on the unique values.\n",
      "If you want the future behaviour and silence this warning, you can specify \"categories='auto'\".\n",
      "In case you used a LabelEncoder before this OneHotEncoder to convert the categories to integers, then you can now use the OneHotEncoder directly.\n",
      " * Warning:  * Something went wrong while precomputing 'precompute_pca_tx'. Will ignore this method. Error message:\n",
      "AttributeError(\"module 'sklearn' has no attribute 'decomposition'\").\n",
      " * Warning: Can't extract feature 'mad'.\n",
      " Exception message: AttributeError(\"module 'scipy.stats' has no attribute 'median_absolute_deviation'\").\n",
      " Will set it as 'np.nan' for all summary functions.\n",
      " * Warning: Mean of empty slice.\n",
      " * Warning: invalid value encountered in double_scalars\n",
      " * Warning: Can't summarize feature 'mad' with summary 'mean'. Will set it as 'np.nan'.\n",
      " * Warning: Can't summarize feature 'mad' with summary 'sd'. Will set it as 'np.nan'.\n",
      " * Warning: Can't extract feature 'leaves'.\n",
      " Exception message: AttributeError(\"'sklearn.tree._tree.Tree' object has no attribute 'n_leaves'\").\n",
      " * Warning: Can't extract feature 'leaves_homo'.\n",
      " Exception message: AttributeError(\"'sklearn.tree._tree.Tree' object has no attribute 'n_leaves'\").\n",
      " Will set it as 'np.nan' for all summary functions.\n",
      " * Warning: Can't summarize feature 'leaves_homo' with summary 'mean'. Will set it as 'np.nan'.\n",
      " * Warning: Can't summarize feature 'leaves_homo' with summary 'sd'. Will set it as 'np.nan'.\n",
      " * Warning: Can't extract feature 'leaves_per_class'.\n",
      " Exception message: AttributeError(\"'sklearn.tree._tree.Tree' object has no attribute 'n_leaves'\").\n",
      " Will set it as 'np.nan' for all summary functions.\n",
      " * Warning: Can't summarize feature 'leaves_per_class' with summary 'mean'. Will set it as 'np.nan'.\n",
      " * Warning: Can't summarize feature 'leaves_per_class' with summary 'sd'. Will set it as 'np.nan'.\n",
      " * Warning: Can't extract feature 'nodes'.\n",
      " Exception message: AttributeError(\"'sklearn.tree._tree.Tree' object has no attribute 'n_leaves'\").\n",
      " * Warning: Can't extract feature 'nodes_per_attr'.\n",
      " Exception message: AttributeError(\"'sklearn.tree._tree.Tree' object has no attribute 'n_leaves'\").\n",
      " * Warning: Can't extract feature 'nodes_per_inst'.\n",
      " Exception message: AttributeError(\"'sklearn.tree._tree.Tree' object has no attribute 'n_leaves'\").\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(['attr_conc.mean', 'attr_conc.sd', 'attr_ent.mean', 'attr_ent.sd', 'attr_to_inst', 'best_node.mean', 'best_node.mean.relative', 'best_node.sd', 'best_node.sd.relative', 'c1', 'c2', 'can_cor.mean', 'can_cor.sd', 'cat_to_num', 'ch', 'class_conc.mean', 'class_conc.sd', 'class_ent', 'cls_coef', 'cohesiveness.mean', 'cohesiveness.sd', 'conceptvar.mean', 'conceptvar.sd', 'cor.mean', 'cor.sd', 'cov.mean', 'cov.sd', 'density', 'eigenvalues.mean', 'eigenvalues.sd', 'elite_nn.mean', 'elite_nn.mean.relative', 'elite_nn.sd', 'elite_nn.sd.relative', 'eq_num_attr', 'f1.mean', 'f1.sd', 'f1v.mean', 'f1v.sd', 'f2.mean', 'f2.sd', 'f3.mean', 'f3.sd', 'f4.mean', 'f4.sd', 'freq_class.mean', 'freq_class.sd', 'g_mean.mean', 'g_mean.sd', 'gravity', 'h_mean.mean', 'h_mean.sd', 'hubs.mean', 'hubs.sd', 'impconceptvar.mean', 'impconceptvar.sd', 'inst_to_attr', 'int', 'iq_range.mean', 'iq_range.sd', 'joint_ent.mean', 'joint_ent.sd', 'kurtosis.mean', 'kurtosis.sd', 'l1.mean', 'l1.sd', 'l2.mean', 'l2.sd', 'l3.mean', 'l3.sd', 'leaves', 'leaves_branch.mean', 'leaves_branch.sd', 'leaves_corrob.mean', 'leaves_corrob.sd', 'leaves_homo.mean', 'leaves_homo.sd', 'leaves_per_class.mean', 'leaves_per_class.sd', 'lh_trace', 'linear_discr.mean', 'linear_discr.mean.relative', 'linear_discr.sd', 'linear_discr.sd.relative', 'lsc', 'mad.mean', 'mad.sd', 'max.mean', 'max.sd', 'mean.mean', 'mean.sd', 'median.mean', 'median.sd', 'min.mean', 'min.sd', 'mut_inf.mean', 'mut_inf.sd', 'n1', 'n2.mean', 'n2.sd', 'n3.mean', 'n3.sd', 'n4.mean', 'n4.sd', 'naive_bayes.mean', 'naive_bayes.mean.relative', 'naive_bayes.sd', 'naive_bayes.sd.relative', 'nodes', 'nodes_per_attr', 'nodes_per_inst', 'nodes_per_level.mean', 'nodes_per_level.sd', 'nodes_repeated.mean', 'nodes_repeated.sd', 'nr_attr', 'nr_bin', 'nr_cat', 'nr_class', 'nr_cor_attr', 'nr_disc', 'nr_inst', 'nr_norm', 'nr_num', 'nr_outliers', 'nre', 'ns_ratio', 'num_to_cat', 'one_itemset.mean', 'one_itemset.sd', 'one_nn.mean', 'one_nn.mean.relative', 'one_nn.sd', 'one_nn.sd.relative', 'p_trace', 'pb', 'random_node.mean', 'random_node.mean.relative', 'random_node.sd', 'random_node.sd.relative', 'range.mean', 'range.sd', 'roy_root', 'sc', 'sd.mean', 'sd.sd', 'sd_ratio', 'sil', 'skewness.mean', 'skewness.sd', 'sparsity.mean', 'sparsity.sd', 't1.mean', 't1.sd', 't2', 't3', 't4', 't_mean.mean', 't_mean.sd', 'tree_depth.mean', 'tree_depth.sd', 'tree_imbalance.mean', 'tree_imbalance.sd', 'tree_shape.mean', 'tree_shape.sd', 'two_itemset.mean', 'two_itemset.sd', 'var.mean', 'var.sd', 'var_importance.mean', 'var_importance.sd', 'vdb', 'vdu', 'w_lambda', 'wg_dist.mean', 'wg_dist.sd', 'worst_node.mean', 'worst_node.mean.relative', 'worst_node.sd', 'worst_node.sd.relative'], [0.20980476831180148, 0.1195879817732128, 2.2771912775084115, 0.06103943244855649, 0.02666666666666667, 0.6666666666666667, 3.0, 1.1702778228589004e-16, 1.0, 0.9999999999999998, 0.0, 0.7280089560229875, 0.3631869218945755, 0.0, nan, 0.27347384133126745, 0.14091096327223987, 1.584962500721156, 0.9029511519485134, 67.10333333333334, 5.355733510152213, 0.495358313970321, 0.07796805526728046, 0.594116025760156, 0.3375443182856702, 0.5966542132736764, 0.5582672431248461, 0.8487695749440716, 1.1432392617449667, 2.0587713015069755, 0.8866666666666667, 4.0, 0.07730012058189371, 7.0, 1.8780672345507194, 0.2775641932566493, 0.2612622587707819, 0.026799629786085716, 0.03377041736533042, 0.0063817663817663794, 0.011053543615254369, 0.12333333333333334, 0.21361959960016152, 0.043333333333333335, 0.07505553499465135, 0.3333333333333333, 0.0, 3.2230731578977903, 2.0229431040263726, 3.2082811597489393, 2.9783891110628673, 2.145948231748242, 0.9550779395957292, 0.06840960691175269, 42.61, 5.354503216731368, 37.5, 3.322592586185653, 1.7000000000000002, 1.2754084313139324, 3.0182209990602855, 0.3821875549207214, -0.8105361276250795, 0.7326910069728161, 0.004329161758000096, 0.007498328119040367, 0.013333333333333345, 0.023094010767585053, 0.0, 0.0, nan, 3.7777777777777777, 1.2018504251546631, 0.1111111111111111, 0.15051762539834182, nan, nan, nan, nan, 32.4773135181212, 0.9800000000000001, 7.0, 0.04499657051403685, 2.5, 0.8179111111111111, nan, nan, 5.425000000000001, 2.4431878083083722, 3.4645000000000006, 1.918485079431164, 3.6125000000000003, 1.919364043982624, 1.8499999999999999, 1.8083141320025125, 0.8439327791692818, 0.4222019352579773, 0.1, 0.2120684449081955, 0.13514251923631423, 0.04666666666666667, 0.211630508282228, 0.0, 0.0, 0.9533333333333334, 5.0, 0.04499657051403685, 2.5, nan, nan, nan, 1.6, 0.8944271909999159, 2.0, 1.4142135623730951, 4, 0, 0, 3, 0.5, 2, 150, 1, 4, 1, 1.0986122886681096, 1.698308838945616, nan, 0.2, 0.04993563108104261, 0.96, 6.0, 0.05621826951410451, 5.0, 1.1918988203346168, -0.6800495958526898, 0.6266666666666667, 2.0, 0.04661372658534006, 4.0, 3.5750000000000006, 1.6500000000000001, 32.19192247318928, 0, 0.9478670787835934, 0.5712994109375844, 1.2708666438750906, 0.5034774406932957, 0.06273198447775732, 0.29439896290757683, 0.0287147773948895, 0.011032357470087495, 0.015625, 0.02514771177279172, 0.02666666666666667, nan, nan, 3.4705555555555554, 1.9048021402275979, 3.0588235294117645, 1.4348601079588785, 0.19491705385114735, 0.13300709991513865, 0.2708333333333333, 0.10711960313126631, 0.32, 0.0851125499534728, 1.1432392617449665, 1.3325463926454557, 0.25, 0.4487534065700905, 0.7513707094756764, 2.3392212858877218e-05, 0.023438635357730147, 0.4620901765870531, 0.05612193762635788, 0.6066666666666667, 1.0, 0.07336699564097411, 6.0])\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      " * Warning: Can't extract feature 'ch'.\n",
      " Exception message: AttributeError(\"module 'sklearn.metrics' has no attribute 'calinski_harabasz_score'\").\n",
      " * Warning: divide by zero encountered in true_divide\n",
      " * Warning: Can't extract feature 't3'.\n",
      " Exception message: AttributeError(\"module 'sklearn' has no attribute 'decomposition'\").\n",
      " * Warning: Can't extract feature 't4'.\n",
      " Exception message: AttributeError(\"module 'sklearn' has no attribute 'decomposition'\").\n"
     ]
    }
   ],
   "source": [
    "# Load a dataset\n",
    "from sklearn.datasets import load_iris\n",
    "from pymfe.mfe import MFE\n",
    "\n",
    "data = load_iris()\n",
    "y = data.target\n",
    "X = data.data\n",
    "\n",
    "# Extract default measures\n",
    "mfe = MFE()\n",
    "mfe.fit(X, y)\n",
    "ft = mfe.extract()\n",
    "print(ft)\n",
    "\n",
    "# Extract general, statistical and information-theoretic measures\n",
    "mfe = MFE(groups=[\"general\", \"statistical\", \"info-theory\"])\n",
    "mfe.fit(X, y)\n",
    "ft = mfe.extract()\n",
    "print(ft)\n",
    "\n",
    "# Extract all available measures\n",
    "mfe = MFE(groups=\"all\")\n",
    "mfe.fit(X, y)\n",
    "ft = mfe.extract()\n",
    "print(ft)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
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       "      <th>values</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>attr_conc.mean</th>\n",
       "      <td>2.098048e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>attr_conc.sd</th>\n",
       "      <td>1.195880e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>attr_ent.mean</th>\n",
       "      <td>2.277191e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>attr_ent.sd</th>\n",
       "      <td>6.103943e-02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>attr_to_inst</th>\n",
       "      <td>2.666667e-02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>best_node.mean</th>\n",
       "      <td>6.666667e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>best_node.mean.relative</th>\n",
       "      <td>3.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>best_node.sd</th>\n",
       "      <td>1.170278e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>best_node.sd.relative</th>\n",
       "      <td>1.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>c1</th>\n",
       "      <td>1.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>c2</th>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>can_cor.mean</th>\n",
       "      <td>7.280090e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>can_cor.sd</th>\n",
       "      <td>3.631869e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>cat_to_num</th>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ch</th>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>class_conc.mean</th>\n",
       "      <td>2.734738e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>class_conc.sd</th>\n",
       "      <td>1.409110e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>class_ent</th>\n",
       "      <td>1.584963e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>cls_coef</th>\n",
       "      <td>9.029512e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>cohesiveness.mean</th>\n",
       "      <td>6.710333e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>cohesiveness.sd</th>\n",
       "      <td>5.355734e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>conceptvar.mean</th>\n",
       "      <td>4.953583e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>conceptvar.sd</th>\n",
       "      <td>7.796806e-02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>cor.mean</th>\n",
       "      <td>5.941160e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>cor.sd</th>\n",
       "      <td>3.375443e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>cov.mean</th>\n",
       "      <td>5.966542e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>cov.sd</th>\n",
       "      <td>5.582672e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>density</th>\n",
       "      <td>8.487696e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>eigenvalues.mean</th>\n",
       "      <td>1.143239e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>eigenvalues.sd</th>\n",
       "      <td>2.058771e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sparsity.mean</th>\n",
       "      <td>2.871478e-02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sparsity.sd</th>\n",
       "      <td>1.103236e-02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>t1.mean</th>\n",
       "      <td>1.562500e-02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>t1.sd</th>\n",
       "      <td>2.514771e-02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>t2</th>\n",
       "      <td>2.666667e-02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>t3</th>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>t4</th>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>t_mean.mean</th>\n",
       "      <td>3.470556e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>t_mean.sd</th>\n",
       "      <td>1.904802e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tree_depth.mean</th>\n",
       "      <td>3.058824e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tree_depth.sd</th>\n",
       "      <td>1.434860e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tree_imbalance.mean</th>\n",
       "      <td>1.949171e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tree_imbalance.sd</th>\n",
       "      <td>1.330071e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tree_shape.mean</th>\n",
       "      <td>2.708333e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>tree_shape.sd</th>\n",
       "      <td>1.071196e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>two_itemset.mean</th>\n",
       "      <td>3.200000e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>two_itemset.sd</th>\n",
       "      <td>8.511255e-02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>var.mean</th>\n",
       "      <td>1.143239e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>var.sd</th>\n",
       "      <td>1.332546e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>var_importance.mean</th>\n",
       "      <td>2.500000e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>var_importance.sd</th>\n",
       "      <td>4.487534e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>vdb</th>\n",
       "      <td>7.513707e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>vdu</th>\n",
       "      <td>2.339221e-05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>w_lambda</th>\n",
       "      <td>2.343864e-02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>wg_dist.mean</th>\n",
       "      <td>4.620902e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>wg_dist.sd</th>\n",
       "      <td>5.612194e-02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>worst_node.mean</th>\n",
       "      <td>6.066667e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>worst_node.mean.relative</th>\n",
       "      <td>1.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>worst_node.sd</th>\n",
       "      <td>7.336700e-02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>worst_node.sd.relative</th>\n",
       "      <td>6.000000e+00</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>180 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                values\n",
       "attr_conc.mean            2.098048e-01\n",
       "attr_conc.sd              1.195880e-01\n",
       "attr_ent.mean             2.277191e+00\n",
       "attr_ent.sd               6.103943e-02\n",
       "attr_to_inst              2.666667e-02\n",
       "best_node.mean            6.666667e-01\n",
       "best_node.mean.relative   3.000000e+00\n",
       "best_node.sd              1.170278e-16\n",
       "best_node.sd.relative     1.000000e+00\n",
       "c1                        1.000000e+00\n",
       "c2                        0.000000e+00\n",
       "can_cor.mean              7.280090e-01\n",
       "can_cor.sd                3.631869e-01\n",
       "cat_to_num                0.000000e+00\n",
       "ch                                 NaN\n",
       "class_conc.mean           2.734738e-01\n",
       "class_conc.sd             1.409110e-01\n",
       "class_ent                 1.584963e+00\n",
       "cls_coef                  9.029512e-01\n",
       "cohesiveness.mean         6.710333e+01\n",
       "cohesiveness.sd           5.355734e+00\n",
       "conceptvar.mean           4.953583e-01\n",
       "conceptvar.sd             7.796806e-02\n",
       "cor.mean                  5.941160e-01\n",
       "cor.sd                    3.375443e-01\n",
       "cov.mean                  5.966542e-01\n",
       "cov.sd                    5.582672e-01\n",
       "density                   8.487696e-01\n",
       "eigenvalues.mean          1.143239e+00\n",
       "eigenvalues.sd            2.058771e+00\n",
       "...                                ...\n",
       "sparsity.mean             2.871478e-02\n",
       "sparsity.sd               1.103236e-02\n",
       "t1.mean                   1.562500e-02\n",
       "t1.sd                     2.514771e-02\n",
       "t2                        2.666667e-02\n",
       "t3                                 NaN\n",
       "t4                                 NaN\n",
       "t_mean.mean               3.470556e+00\n",
       "t_mean.sd                 1.904802e+00\n",
       "tree_depth.mean           3.058824e+00\n",
       "tree_depth.sd             1.434860e+00\n",
       "tree_imbalance.mean       1.949171e-01\n",
       "tree_imbalance.sd         1.330071e-01\n",
       "tree_shape.mean           2.708333e-01\n",
       "tree_shape.sd             1.071196e-01\n",
       "two_itemset.mean          3.200000e-01\n",
       "two_itemset.sd            8.511255e-02\n",
       "var.mean                  1.143239e+00\n",
       "var.sd                    1.332546e+00\n",
       "var_importance.mean       2.500000e-01\n",
       "var_importance.sd         4.487534e-01\n",
       "vdb                       7.513707e-01\n",
       "vdu                       2.339221e-05\n",
       "w_lambda                  2.343864e-02\n",
       "wg_dist.mean              4.620902e-01\n",
       "wg_dist.sd                5.612194e-02\n",
       "worst_node.mean           6.066667e-01\n",
       "worst_node.mean.relative  1.000000e+00\n",
       "worst_node.sd             7.336700e-02\n",
       "worst_node.sd.relative    6.000000e+00\n",
       "\n",
       "[180 rows x 1 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import pandas as pd\n",
    "\n",
    "pd.DataFrame({'values': ft[1]}, index=ft[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<div>\n",
       "<style scoped>\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th>ID</th>\n",
       "      <th>GSM4045109</th>\n",
       "      <th>GSM4045110</th>\n",
       "      <th>GSM4045111</th>\n",
       "      <th>GSM4045112</th>\n",
       "      <th>GSM4045113</th>\n",
       "      <th>GSM4045114</th>\n",
       "      <th>GSM4045115</th>\n",
       "      <th>GSM4045116</th>\n",
       "      <th>GSM4045117</th>\n",
       "      <th>GSM4045118</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>t_14_20cyto</th>\n",
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       "    <tr>\n",
       "      <th>hyperdiploidcyto</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "    <tr>\n",
       "      <th>del1qcyto</th>\n",
       "      <td>0</td>\n",
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       "      <td>1</td>\n",
       "      <td>0</td>\n",
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       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>del13qcyto</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>b2m</th>\n",
       "      <td>3</td>\n",
       "      <td>2.3</td>\n",
       "      <td>3.5</td>\n",
       "      <td>3.5</td>\n",
       "      <td>1.96</td>\n",
       "      <td>3.2</td>\n",
       "      <td>4.9</td>\n",
       "      <td>2.2</td>\n",
       "      <td>2.2</td>\n",
       "      <td>3.2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>albumin</th>\n",
       "      <td>4.5</td>\n",
       "      <td>4</td>\n",
       "      <td>4.5</td>\n",
       "      <td>4.5</td>\n",
       "      <td>3.7</td>\n",
       "      <td>3.9</td>\n",
       "      <td>3.1</td>\n",
       "      <td>4.9</td>\n",
       "      <td>4.9</td>\n",
       "      <td>4.9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>t_12_14cyto</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>recrev</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>del11qcyto</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>t_11_14cyto</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>amp1qcyto</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>x1qpluscyto</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
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       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ldh</th>\n",
       "      <td>146</td>\n",
       "      <td>238</td>\n",
       "      <td>133</td>\n",
       "      <td>133</td>\n",
       "      <td>133</td>\n",
       "      <td>162</td>\n",
       "      <td>296</td>\n",
       "      <td>145</td>\n",
       "      <td>145</td>\n",
       "      <td>108</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>age_at_diagnosis</th>\n",
       "      <td>63.3</td>\n",
       "      <td>64.8</td>\n",
       "      <td>55</td>\n",
       "      <td>55</td>\n",
       "      <td>54.7</td>\n",
       "      <td>61.5</td>\n",
       "      <td>60.2</td>\n",
       "      <td>60.8</td>\n",
       "      <td>60.8</td>\n",
       "      <td>52.5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>t_14_16cyto</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>iss</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>del17pcyto</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>del1p32cyto</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>del1pcyto</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>del16qcyto</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>myc_8q24cyto</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>race_asian</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>race_black</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>race_hispanic</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>race_white_caucasian</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>treatment</th>\n",
       "      <td>thalidomide</td>\n",
       "      <td>thalidomide</td>\n",
       "      <td>thalidomide</td>\n",
       "      <td>thalidomide</td>\n",
       "      <td>thalidomide</td>\n",
       "      <td>thalidomide</td>\n",
       "      <td>thalidomide</td>\n",
       "      <td>thalidomide</td>\n",
       "      <td>thalidomide</td>\n",
       "      <td>thalidomide</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>gender</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>transplant</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "ID                     GSM4045109   GSM4045110   GSM4045111   GSM4045112  \\\n",
       "t_14_20cyto                     0            0            0            0   \n",
       "hyperdiploidcyto                0            0            1            1   \n",
       "del1qcyto                       0            0            1            1   \n",
       "del13qcyto                      0            0            1            1   \n",
       "b2m                             3          2.3          3.5          3.5   \n",
       "albumin                       4.5            4          4.5          4.5   \n",
       "t_12_14cyto                     0            0            0            0   \n",
       "recrev                          0            0            0            0   \n",
       "del11qcyto                      0            0            0            0   \n",
       "t_11_14cyto                     0            0            0            0   \n",
       "amp1qcyto                       0            0            0            0   \n",
       "x1qpluscyto                     0            0            1            1   \n",
       "ldh                           146          238          133          133   \n",
       "age_at_diagnosis             63.3         64.8           55           55   \n",
       "t_14_16cyto                     0            0            0            0   \n",
       "iss                             1            1            2            2   \n",
       "del17pcyto                      0            0            0            0   \n",
       "del1p32cyto                     0            0            1            1   \n",
       "del1pcyto                       0            0            1            1   \n",
       "del16qcyto                      0            0            0            0   \n",
       "myc_8q24cyto                    0            0            1            1   \n",
       "race_asian                      0            0            0            0   \n",
       "race_black                      0            0            0            0   \n",
       "race_hispanic                   0            0            0            0   \n",
       "race_white_caucasian            1            1            1            1   \n",
       "treatment             thalidomide  thalidomide  thalidomide  thalidomide   \n",
       "gender                          1            1            0            0   \n",
       "transplant                      1            1            1            1   \n",
       "\n",
       "ID                     GSM4045113   GSM4045114   GSM4045115   GSM4045116  \\\n",
       "t_14_20cyto                     0            0            0            0   \n",
       "hyperdiploidcyto                0            0            0            0   \n",
       "del1qcyto                       0            0            0            1   \n",
       "del13qcyto                      0            0            0            1   \n",
       "b2m                          1.96          3.2          4.9          2.2   \n",
       "albumin                       3.7          3.9          3.1          4.9   \n",
       "t_12_14cyto                     0            0            0            0   \n",
       "recrev                          0            0            0            0   \n",
       "del11qcyto                      0            0            0            0   \n",
       "t_11_14cyto                     0            0            0            0   \n",
       "amp1qcyto                       0            0            0            0   \n",
       "x1qpluscyto                     0            1            0            1   \n",
       "ldh                           133          162          296          145   \n",
       "age_at_diagnosis             54.7         61.5         60.2         60.8   \n",
       "t_14_16cyto                     0            0            0            0   \n",
       "iss                             1            1            2            1   \n",
       "del17pcyto                      0            0            0            0   \n",
       "del1p32cyto                     0            0            0            1   \n",
       "del1pcyto                       0            0            0            1   \n",
       "del16qcyto                      0            0            0            0   \n",
       "myc_8q24cyto                    0            0            0            0   \n",
       "race_asian                      0            0            0            0   \n",
       "race_black                      0            0            1            0   \n",
       "race_hispanic                   0            0            0            0   \n",
       "race_white_caucasian            1            1            0            1   \n",
       "treatment             thalidomide  thalidomide  thalidomide  thalidomide   \n",
       "gender                          0            0            0            0   \n",
       "transplant                      1            1            1            1   \n",
       "\n",
       "ID                     GSM4045117   GSM4045118  \n",
       "t_14_20cyto                     0            0  \n",
       "hyperdiploidcyto                0            0  \n",
       "del1qcyto                       1            0  \n",
       "del13qcyto                      1            0  \n",
       "b2m                           2.2          3.2  \n",
       "albumin                       4.9          4.9  \n",
       "t_12_14cyto                     0            0  \n",
       "recrev                          0            0  \n",
       "del11qcyto                      0            0  \n",
       "t_11_14cyto                     0            0  \n",
       "amp1qcyto                       0            0  \n",
       "x1qpluscyto                     1            0  \n",
       "ldh                           145          108  \n",
       "age_at_diagnosis             60.8         52.5  \n",
       "t_14_16cyto                     0            0  \n",
       "iss                             1            1  \n",
       "del17pcyto                      0            0  \n",
       "del1p32cyto                     1            0  \n",
       "del1pcyto                       1            0  \n",
       "del16qcyto                      0            0  \n",
       "myc_8q24cyto                    0            0  \n",
       "race_asian                      0            0  \n",
       "race_black                      0            0  \n",
       "race_hispanic                   0            0  \n",
       "race_white_caucasian            1            1  \n",
       "treatment             thalidomide  thalidomide  \n",
       "gender                          0            0  \n",
       "transplant                      1            1  "
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from data import load_data_gse136400\n",
    "\n",
    "c, g, o = load_data_gse136400()\n",
    "\n",
    "c.head(10).T"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>GSM4045109</th>\n",
       "      <th>GSM4045110</th>\n",
       "      <th>GSM4045111</th>\n",
       "      <th>GSM4045112</th>\n",
       "      <th>GSM4045113</th>\n",
       "      <th>GSM4045114</th>\n",
       "      <th>GSM4045115</th>\n",
       "      <th>GSM4045116</th>\n",
       "      <th>GSM4045117</th>\n",
       "      <th>GSM4045118</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ID</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>AFFX-BioB-3_at</th>\n",
       "      <td>1.755863e+03</td>\n",
       "      <td>1.051528e+03</td>\n",
       "      <td>7.036322e+02</td>\n",
       "      <td>2.308084e+03</td>\n",
       "      <td>1.456057e+03</td>\n",
       "      <td>2.987627e+03</td>\n",
       "      <td>8.619126e+03</td>\n",
       "      <td>6.851476e+04</td>\n",
       "      <td>2.395435e+03</td>\n",
       "      <td>1.549348e+03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-BioB-5_at</th>\n",
       "      <td>2.609266e+03</td>\n",
       "      <td>8.619696e+02</td>\n",
       "      <td>8.917588e+02</td>\n",
       "      <td>2.243988e+03</td>\n",
       "      <td>1.252745e+03</td>\n",
       "      <td>3.113805e+03</td>\n",
       "      <td>1.375395e+04</td>\n",
       "      <td>6.001064e+04</td>\n",
       "      <td>1.530273e+03</td>\n",
       "      <td>1.574032e+03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-BioB-M_at</th>\n",
       "      <td>4.659923e+03</td>\n",
       "      <td>1.701677e+03</td>\n",
       "      <td>1.386187e+03</td>\n",
       "      <td>5.372558e+03</td>\n",
       "      <td>2.825406e+03</td>\n",
       "      <td>7.320880e+03</td>\n",
       "      <td>2.139660e+04</td>\n",
       "      <td>1.254495e+05</td>\n",
       "      <td>3.307275e+03</td>\n",
       "      <td>4.248116e+03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-BioC-3_at</th>\n",
       "      <td>1.748921e+04</td>\n",
       "      <td>6.778294e+03</td>\n",
       "      <td>4.773245e+03</td>\n",
       "      <td>1.627430e+04</td>\n",
       "      <td>1.169582e+04</td>\n",
       "      <td>2.147305e+04</td>\n",
       "      <td>6.747849e+04</td>\n",
       "      <td>2.500523e+05</td>\n",
       "      <td>1.359552e+04</td>\n",
       "      <td>1.416617e+04</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-BioC-5_at</th>\n",
       "      <td>1.115263e+04</td>\n",
       "      <td>4.549913e+03</td>\n",
       "      <td>4.474977e+03</td>\n",
       "      <td>1.135881e+04</td>\n",
       "      <td>6.828429e+03</td>\n",
       "      <td>1.362722e+04</td>\n",
       "      <td>4.363743e+04</td>\n",
       "      <td>2.163762e+05</td>\n",
       "      <td>7.453435e+03</td>\n",
       "      <td>7.641976e+03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-BioDn-3_at</th>\n",
       "      <td>1.796681e+05</td>\n",
       "      <td>1.122930e+05</td>\n",
       "      <td>4.220047e+04</td>\n",
       "      <td>1.690839e+05</td>\n",
       "      <td>1.070336e+05</td>\n",
       "      <td>1.551901e+05</td>\n",
       "      <td>3.844489e+05</td>\n",
       "      <td>9.922842e+05</td>\n",
       "      <td>1.374475e+05</td>\n",
       "      <td>1.055391e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-BioDn-5_at</th>\n",
       "      <td>4.038222e+04</td>\n",
       "      <td>1.115087e+04</td>\n",
       "      <td>6.377619e+03</td>\n",
       "      <td>3.466787e+04</td>\n",
       "      <td>2.023786e+04</td>\n",
       "      <td>3.971513e+04</td>\n",
       "      <td>9.817101e+04</td>\n",
       "      <td>3.929779e+05</td>\n",
       "      <td>2.371066e+04</td>\n",
       "      <td>2.417201e+04</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-CreX-3_at</th>\n",
       "      <td>5.466199e+05</td>\n",
       "      <td>3.840433e+05</td>\n",
       "      <td>1.072299e+05</td>\n",
       "      <td>5.520122e+05</td>\n",
       "      <td>4.616768e+05</td>\n",
       "      <td>7.120973e+05</td>\n",
       "      <td>9.597436e+05</td>\n",
       "      <td>1.637867e+06</td>\n",
       "      <td>4.925552e+05</td>\n",
       "      <td>5.121528e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-CreX-5_at</th>\n",
       "      <td>4.124788e+05</td>\n",
       "      <td>2.596821e+05</td>\n",
       "      <td>8.421221e+04</td>\n",
       "      <td>3.595671e+05</td>\n",
       "      <td>2.780945e+05</td>\n",
       "      <td>4.919018e+05</td>\n",
       "      <td>7.818489e+05</td>\n",
       "      <td>1.210629e+06</td>\n",
       "      <td>3.394657e+05</td>\n",
       "      <td>3.521837e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-DapX-3_at</th>\n",
       "      <td>3.894212e+01</td>\n",
       "      <td>7.236191e+01</td>\n",
       "      <td>8.733181e+01</td>\n",
       "      <td>3.849554e+01</td>\n",
       "      <td>2.586933e+01</td>\n",
       "      <td>4.976531e+01</td>\n",
       "      <td>1.373165e+02</td>\n",
       "      <td>1.157588e+02</td>\n",
       "      <td>4.061084e+01</td>\n",
       "      <td>5.164075e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-DapX-5_at</th>\n",
       "      <td>5.563402e+01</td>\n",
       "      <td>4.068950e+01</td>\n",
       "      <td>8.341774e+01</td>\n",
       "      <td>3.350288e+01</td>\n",
       "      <td>4.898914e+01</td>\n",
       "      <td>6.775167e+01</td>\n",
       "      <td>3.004492e+02</td>\n",
       "      <td>9.462634e+01</td>\n",
       "      <td>4.003301e+01</td>\n",
       "      <td>3.785649e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-DapX-M_at</th>\n",
       "      <td>3.460741e+01</td>\n",
       "      <td>5.899745e+01</td>\n",
       "      <td>7.992320e+01</td>\n",
       "      <td>2.986146e+01</td>\n",
       "      <td>4.488523e+01</td>\n",
       "      <td>4.943990e+01</td>\n",
       "      <td>1.000536e+02</td>\n",
       "      <td>2.600284e+02</td>\n",
       "      <td>5.734094e+01</td>\n",
       "      <td>5.963054e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-HSAC07/X00351_3_at</th>\n",
       "      <td>6.868457e+05</td>\n",
       "      <td>6.909729e+05</td>\n",
       "      <td>2.234569e+05</td>\n",
       "      <td>7.430455e+05</td>\n",
       "      <td>5.791595e+05</td>\n",
       "      <td>8.414095e+05</td>\n",
       "      <td>5.643952e+05</td>\n",
       "      <td>6.761790e+05</td>\n",
       "      <td>6.886985e+05</td>\n",
       "      <td>6.887205e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-HSAC07/X00351_5_at</th>\n",
       "      <td>1.972463e+05</td>\n",
       "      <td>1.142630e+05</td>\n",
       "      <td>2.374328e+04</td>\n",
       "      <td>1.878236e+05</td>\n",
       "      <td>2.002396e+05</td>\n",
       "      <td>2.407423e+05</td>\n",
       "      <td>3.061958e+04</td>\n",
       "      <td>3.730134e+04</td>\n",
       "      <td>2.391718e+05</td>\n",
       "      <td>2.343083e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-HSAC07/X00351_M_at</th>\n",
       "      <td>5.489923e+05</td>\n",
       "      <td>3.414072e+05</td>\n",
       "      <td>1.088369e+05</td>\n",
       "      <td>4.707339e+05</td>\n",
       "      <td>4.900337e+05</td>\n",
       "      <td>5.827385e+05</td>\n",
       "      <td>1.091917e+05</td>\n",
       "      <td>1.522655e+05</td>\n",
       "      <td>5.596867e+05</td>\n",
       "      <td>5.519344e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-hum_alu_at</th>\n",
       "      <td>1.854373e+06</td>\n",
       "      <td>1.912195e+06</td>\n",
       "      <td>1.016447e+06</td>\n",
       "      <td>1.798335e+06</td>\n",
       "      <td>1.705037e+06</td>\n",
       "      <td>1.821483e+06</td>\n",
       "      <td>2.187894e+06</td>\n",
       "      <td>1.744950e+06</td>\n",
       "      <td>1.694161e+06</td>\n",
       "      <td>1.671716e+06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-HUMGAPDH/M33197_3_at</th>\n",
       "      <td>2.832526e+05</td>\n",
       "      <td>4.096226e+05</td>\n",
       "      <td>1.442499e+05</td>\n",
       "      <td>4.352737e+05</td>\n",
       "      <td>3.411160e+05</td>\n",
       "      <td>4.181495e+05</td>\n",
       "      <td>1.848463e+05</td>\n",
       "      <td>4.208204e+05</td>\n",
       "      <td>3.889034e+05</td>\n",
       "      <td>3.487891e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-HUMGAPDH/M33197_5_at</th>\n",
       "      <td>2.191365e+05</td>\n",
       "      <td>1.986953e+05</td>\n",
       "      <td>2.883444e+04</td>\n",
       "      <td>2.113432e+05</td>\n",
       "      <td>3.011332e+05</td>\n",
       "      <td>3.958054e+05</td>\n",
       "      <td>5.206185e+04</td>\n",
       "      <td>1.480541e+05</td>\n",
       "      <td>3.724460e+05</td>\n",
       "      <td>3.086704e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-HUMGAPDH/M33197_M_at</th>\n",
       "      <td>2.384620e+05</td>\n",
       "      <td>3.097419e+05</td>\n",
       "      <td>6.115301e+04</td>\n",
       "      <td>3.013173e+05</td>\n",
       "      <td>3.327942e+05</td>\n",
       "      <td>3.666560e+05</td>\n",
       "      <td>6.934988e+04</td>\n",
       "      <td>1.995295e+05</td>\n",
       "      <td>3.846219e+05</td>\n",
       "      <td>3.026603e+05</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-HUMISGF3A/M97935_3_at</th>\n",
       "      <td>7.371359e+04</td>\n",
       "      <td>2.724134e+04</td>\n",
       "      <td>5.598092e+03</td>\n",
       "      <td>1.268083e+04</td>\n",
       "      <td>3.452911e+04</td>\n",
       "      <td>3.035638e+04</td>\n",
       "      <td>1.364868e+04</td>\n",
       "      <td>2.129259e+04</td>\n",
       "      <td>2.659678e+04</td>\n",
       "      <td>2.164598e+04</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-HUMISGF3A/M97935_5_at</th>\n",
       "      <td>8.081984e+02</td>\n",
       "      <td>1.294272e+02</td>\n",
       "      <td>1.072945e+02</td>\n",
       "      <td>1.599489e+02</td>\n",
       "      <td>2.876874e+02</td>\n",
       "      <td>2.012268e+02</td>\n",
       "      <td>1.460646e+02</td>\n",
       "      <td>1.435098e+02</td>\n",
       "      <td>2.556011e+02</td>\n",
       "      <td>2.162182e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-HUMISGF3A/M97935_MA_at</th>\n",
       "      <td>8.839185e+03</td>\n",
       "      <td>2.402806e+03</td>\n",
       "      <td>1.264187e+03</td>\n",
       "      <td>3.286319e+03</td>\n",
       "      <td>2.453882e+03</td>\n",
       "      <td>2.828798e+03</td>\n",
       "      <td>2.598615e+03</td>\n",
       "      <td>1.249116e+03</td>\n",
       "      <td>2.621227e+03</td>\n",
       "      <td>2.865892e+03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-HUMISGF3A/M97935_MB_at</th>\n",
       "      <td>5.896802e+03</td>\n",
       "      <td>1.122953e+03</td>\n",
       "      <td>1.785512e+02</td>\n",
       "      <td>1.081362e+03</td>\n",
       "      <td>1.461913e+03</td>\n",
       "      <td>1.595176e+03</td>\n",
       "      <td>3.685668e+02</td>\n",
       "      <td>2.415570e+02</td>\n",
       "      <td>9.368665e+02</td>\n",
       "      <td>1.259107e+03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-HUMRGE/M10098_3_at</th>\n",
       "      <td>7.909970e+03</td>\n",
       "      <td>1.136161e+04</td>\n",
       "      <td>1.458287e+04</td>\n",
       "      <td>4.819461e+04</td>\n",
       "      <td>1.324270e+04</td>\n",
       "      <td>9.364781e+03</td>\n",
       "      <td>1.168455e+04</td>\n",
       "      <td>5.652781e+04</td>\n",
       "      <td>5.963767e+03</td>\n",
       "      <td>2.299509e+04</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-HUMRGE/M10098_5_at</th>\n",
       "      <td>3.932404e+03</td>\n",
       "      <td>6.275596e+03</td>\n",
       "      <td>7.927674e+03</td>\n",
       "      <td>5.173239e+04</td>\n",
       "      <td>2.823140e+04</td>\n",
       "      <td>8.260244e+03</td>\n",
       "      <td>4.612189e+03</td>\n",
       "      <td>1.063473e+05</td>\n",
       "      <td>8.587409e+03</td>\n",
       "      <td>1.340800e+04</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-HUMRGE/M10098_M_at</th>\n",
       "      <td>7.568390e+03</td>\n",
       "      <td>7.466982e+03</td>\n",
       "      <td>9.892887e+03</td>\n",
       "      <td>4.004570e+04</td>\n",
       "      <td>1.751118e+04</td>\n",
       "      <td>7.960958e+03</td>\n",
       "      <td>6.481459e+03</td>\n",
       "      <td>7.755317e+04</td>\n",
       "      <td>5.898283e+03</td>\n",
       "      <td>1.210365e+04</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-LysX-3_at</th>\n",
       "      <td>3.531883e+01</td>\n",
       "      <td>3.673993e+01</td>\n",
       "      <td>4.246824e+01</td>\n",
       "      <td>2.662290e+01</td>\n",
       "      <td>4.417314e+01</td>\n",
       "      <td>3.453204e+01</td>\n",
       "      <td>8.051537e+01</td>\n",
       "      <td>2.834344e+02</td>\n",
       "      <td>3.385307e+01</td>\n",
       "      <td>3.061428e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-LysX-5_at</th>\n",
       "      <td>4.490146e+01</td>\n",
       "      <td>3.093758e+01</td>\n",
       "      <td>4.479816e+01</td>\n",
       "      <td>2.658205e+01</td>\n",
       "      <td>2.818668e+01</td>\n",
       "      <td>2.602906e+01</td>\n",
       "      <td>6.342960e+01</td>\n",
       "      <td>3.432736e+02</td>\n",
       "      <td>4.189544e+01</td>\n",
       "      <td>3.094531e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-LysX-M_at</th>\n",
       "      <td>4.842260e+01</td>\n",
       "      <td>8.224320e+01</td>\n",
       "      <td>1.276286e+02</td>\n",
       "      <td>5.954139e+01</td>\n",
       "      <td>5.006925e+01</td>\n",
       "      <td>5.757026e+01</td>\n",
       "      <td>3.259435e+02</td>\n",
       "      <td>1.890808e+02</td>\n",
       "      <td>3.887226e+01</td>\n",
       "      <td>5.385793e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AFFX-M27830_3_at</th>\n",
       "      <td>4.255318e+02</td>\n",
       "      <td>1.193517e+03</td>\n",
       "      <td>3.570117e+03</td>\n",
       "      <td>8.155367e+02</td>\n",
       "      <td>9.297030e+02</td>\n",
       "      <td>6.674073e+02</td>\n",
       "      <td>1.290183e+03</td>\n",
       "      <td>8.238710e+02</td>\n",
       "      <td>5.888021e+02</td>\n",
       "      <td>9.541505e+02</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LINC00836</th>\n",
       "      <td>8.380857e+01</td>\n",
       "      <td>1.171674e+02</td>\n",
       "      <td>2.542338e+02</td>\n",
       "      <td>1.058770e+02</td>\n",
       "      <td>1.165537e+02</td>\n",
       "      <td>6.586334e+01</td>\n",
       "      <td>1.878555e+02</td>\n",
       "      <td>6.795693e+01</td>\n",
       "      <td>6.966192e+01</td>\n",
       "      <td>8.563582e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ST3GAL4-AS1</th>\n",
       "      <td>3.021504e+02</td>\n",
       "      <td>3.673940e+02</td>\n",
       "      <td>2.919499e+02</td>\n",
       "      <td>3.745727e+02</td>\n",
       "      <td>2.941575e+02</td>\n",
       "      <td>3.599727e+02</td>\n",
       "      <td>5.035231e+02</td>\n",
       "      <td>3.875506e+02</td>\n",
       "      <td>5.655795e+02</td>\n",
       "      <td>2.765174e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CTBP1-AS</th>\n",
       "      <td>1.411848e+02</td>\n",
       "      <td>1.356484e+02</td>\n",
       "      <td>2.217986e+02</td>\n",
       "      <td>8.892724e+01</td>\n",
       "      <td>1.692691e+02</td>\n",
       "      <td>1.177977e+02</td>\n",
       "      <td>1.936232e+02</td>\n",
       "      <td>2.193928e+02</td>\n",
       "      <td>1.901629e+02</td>\n",
       "      <td>8.401229e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LINC01395</th>\n",
       "      <td>6.671617e+01</td>\n",
       "      <td>6.898182e+01</td>\n",
       "      <td>6.493662e+01</td>\n",
       "      <td>6.443267e+01</td>\n",
       "      <td>7.558109e+01</td>\n",
       "      <td>6.001126e+01</td>\n",
       "      <td>7.382139e+01</td>\n",
       "      <td>1.316112e+02</td>\n",
       "      <td>7.458588e+01</td>\n",
       "      <td>5.880468e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TRG-AS1</th>\n",
       "      <td>1.622814e+03</td>\n",
       "      <td>5.904574e+02</td>\n",
       "      <td>6.321255e+02</td>\n",
       "      <td>7.132672e+02</td>\n",
       "      <td>8.574431e+02</td>\n",
       "      <td>6.427795e+02</td>\n",
       "      <td>7.423100e+02</td>\n",
       "      <td>1.398641e+03</td>\n",
       "      <td>1.008531e+03</td>\n",
       "      <td>1.458032e+03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LINC01127</th>\n",
       "      <td>1.193389e+02</td>\n",
       "      <td>2.513251e+02</td>\n",
       "      <td>2.205077e+02</td>\n",
       "      <td>3.255506e+02</td>\n",
       "      <td>2.400394e+02</td>\n",
       "      <td>3.352030e+02</td>\n",
       "      <td>3.112343e+02</td>\n",
       "      <td>3.041061e+02</td>\n",
       "      <td>4.955021e+02</td>\n",
       "      <td>1.641224e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>GHET1</th>\n",
       "      <td>5.111353e+01</td>\n",
       "      <td>1.094283e+02</td>\n",
       "      <td>1.196598e+02</td>\n",
       "      <td>5.356148e+01</td>\n",
       "      <td>6.643359e+01</td>\n",
       "      <td>4.924642e+01</td>\n",
       "      <td>3.476788e+02</td>\n",
       "      <td>7.425843e+01</td>\n",
       "      <td>5.627091e+01</td>\n",
       "      <td>6.438532e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LINC00934</th>\n",
       "      <td>7.726465e+01</td>\n",
       "      <td>1.649858e+02</td>\n",
       "      <td>1.789765e+02</td>\n",
       "      <td>1.385062e+02</td>\n",
       "      <td>1.435644e+02</td>\n",
       "      <td>8.145322e+01</td>\n",
       "      <td>1.765650e+02</td>\n",
       "      <td>8.070117e+01</td>\n",
       "      <td>1.088027e+02</td>\n",
       "      <td>8.909109e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LINC01097</th>\n",
       "      <td>7.354629e+01</td>\n",
       "      <td>4.954148e+01</td>\n",
       "      <td>9.637506e+01</td>\n",
       "      <td>6.446172e+01</td>\n",
       "      <td>4.992021e+01</td>\n",
       "      <td>4.358246e+01</td>\n",
       "      <td>1.408929e+02</td>\n",
       "      <td>6.608350e+01</td>\n",
       "      <td>5.188158e+01</td>\n",
       "      <td>5.197344e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LINC00950</th>\n",
       "      <td>1.284265e+02</td>\n",
       "      <td>1.817042e+02</td>\n",
       "      <td>3.036536e+02</td>\n",
       "      <td>1.616215e+02</td>\n",
       "      <td>1.684381e+02</td>\n",
       "      <td>9.930234e+01</td>\n",
       "      <td>2.376496e+02</td>\n",
       "      <td>1.634580e+02</td>\n",
       "      <td>1.338300e+02</td>\n",
       "      <td>1.421620e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LINC00997</th>\n",
       "      <td>1.014409e+02</td>\n",
       "      <td>1.755433e+02</td>\n",
       "      <td>2.978431e+02</td>\n",
       "      <td>1.794031e+02</td>\n",
       "      <td>1.295527e+02</td>\n",
       "      <td>1.159935e+02</td>\n",
       "      <td>1.167505e+02</td>\n",
       "      <td>1.881942e+02</td>\n",
       "      <td>1.147452e+02</td>\n",
       "      <td>1.332840e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ARRDC3-AS1</th>\n",
       "      <td>3.878131e+02</td>\n",
       "      <td>5.748631e+02</td>\n",
       "      <td>6.368871e+02</td>\n",
       "      <td>4.753206e+02</td>\n",
       "      <td>3.937129e+02</td>\n",
       "      <td>5.105110e+02</td>\n",
       "      <td>9.479642e+02</td>\n",
       "      <td>1.143480e+03</td>\n",
       "      <td>4.719819e+02</td>\n",
       "      <td>5.338657e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>RASSF1-AS1</th>\n",
       "      <td>2.749528e+02</td>\n",
       "      <td>3.360092e+02</td>\n",
       "      <td>2.906803e+02</td>\n",
       "      <td>2.355413e+02</td>\n",
       "      <td>2.587016e+02</td>\n",
       "      <td>3.664831e+02</td>\n",
       "      <td>5.789443e+02</td>\n",
       "      <td>5.439730e+02</td>\n",
       "      <td>3.129780e+02</td>\n",
       "      <td>2.358641e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EBLN3P</th>\n",
       "      <td>2.748961e+04</td>\n",
       "      <td>9.031401e+03</td>\n",
       "      <td>3.571447e+03</td>\n",
       "      <td>9.166557e+03</td>\n",
       "      <td>1.153876e+04</td>\n",
       "      <td>1.137597e+04</td>\n",
       "      <td>3.367037e+03</td>\n",
       "      <td>5.405570e+03</td>\n",
       "      <td>7.310212e+03</td>\n",
       "      <td>1.836648e+04</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PACRG-AS1</th>\n",
       "      <td>1.570721e+02</td>\n",
       "      <td>1.580482e+02</td>\n",
       "      <td>3.487350e+02</td>\n",
       "      <td>1.636432e+02</td>\n",
       "      <td>1.667425e+02</td>\n",
       "      <td>1.833777e+02</td>\n",
       "      <td>1.734486e+02</td>\n",
       "      <td>2.016184e+02</td>\n",
       "      <td>1.551759e+02</td>\n",
       "      <td>1.641504e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LINC01012</th>\n",
       "      <td>5.440292e+01</td>\n",
       "      <td>7.351251e+01</td>\n",
       "      <td>7.917156e+01</td>\n",
       "      <td>6.873824e+01</td>\n",
       "      <td>6.511249e+01</td>\n",
       "      <td>5.469167e+01</td>\n",
       "      <td>1.268777e+02</td>\n",
       "      <td>6.798058e+01</td>\n",
       "      <td>5.485846e+01</td>\n",
       "      <td>6.461353e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LINC00550</th>\n",
       "      <td>2.346779e+01</td>\n",
       "      <td>2.164096e+01</td>\n",
       "      <td>2.760505e+01</td>\n",
       "      <td>2.510187e+01</td>\n",
       "      <td>2.568066e+01</td>\n",
       "      <td>2.470717e+01</td>\n",
       "      <td>6.144764e+01</td>\n",
       "      <td>4.501257e+01</td>\n",
       "      <td>2.911259e+01</td>\n",
       "      <td>2.196796e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>HCP5B</th>\n",
       "      <td>4.053197e+02</td>\n",
       "      <td>5.272324e+02</td>\n",
       "      <td>3.382034e+02</td>\n",
       "      <td>3.078281e+02</td>\n",
       "      <td>4.898737e+02</td>\n",
       "      <td>3.062724e+02</td>\n",
       "      <td>7.101475e+02</td>\n",
       "      <td>4.502677e+02</td>\n",
       "      <td>4.449688e+02</td>\n",
       "      <td>2.450065e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LINC01144</th>\n",
       "      <td>2.636523e+02</td>\n",
       "      <td>2.293225e+02</td>\n",
       "      <td>6.287470e+02</td>\n",
       "      <td>2.069933e+02</td>\n",
       "      <td>3.496224e+02</td>\n",
       "      <td>1.883269e+02</td>\n",
       "      <td>5.226923e+02</td>\n",
       "      <td>4.543992e+02</td>\n",
       "      <td>3.743490e+02</td>\n",
       "      <td>2.386898e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TRBV25-1</th>\n",
       "      <td>2.768496e+01</td>\n",
       "      <td>2.618768e+01</td>\n",
       "      <td>4.219478e+01</td>\n",
       "      <td>2.795604e+01</td>\n",
       "      <td>3.153416e+01</td>\n",
       "      <td>2.809673e+01</td>\n",
       "      <td>4.009371e+01</td>\n",
       "      <td>4.174284e+01</td>\n",
       "      <td>2.713000e+01</td>\n",
       "      <td>2.952858e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>FRG1CP</th>\n",
       "      <td>4.471846e+03</td>\n",
       "      <td>3.079122e+02</td>\n",
       "      <td>2.020928e+03</td>\n",
       "      <td>2.423757e+03</td>\n",
       "      <td>2.926161e+02</td>\n",
       "      <td>1.428656e+03</td>\n",
       "      <td>6.994452e+02</td>\n",
       "      <td>1.330983e+03</td>\n",
       "      <td>1.619610e+03</td>\n",
       "      <td>2.675468e+03</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KLF18</th>\n",
       "      <td>7.235463e+01</td>\n",
       "      <td>8.309179e+01</td>\n",
       "      <td>7.866811e+01</td>\n",
       "      <td>7.715398e+01</td>\n",
       "      <td>8.868531e+01</td>\n",
       "      <td>6.613909e+01</td>\n",
       "      <td>1.543208e+02</td>\n",
       "      <td>9.700119e+01</td>\n",
       "      <td>6.998682e+01</td>\n",
       "      <td>6.855877e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>OR5AK4P</th>\n",
       "      <td>2.037513e+02</td>\n",
       "      <td>4.324295e+02</td>\n",
       "      <td>8.130921e+02</td>\n",
       "      <td>2.029329e+02</td>\n",
       "      <td>4.001370e+02</td>\n",
       "      <td>2.494575e+02</td>\n",
       "      <td>9.473338e+02</td>\n",
       "      <td>4.334772e+02</td>\n",
       "      <td>3.020590e+02</td>\n",
       "      <td>3.134657e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000283703_at</th>\n",
       "      <td>1.258596e+02</td>\n",
       "      <td>1.301257e+02</td>\n",
       "      <td>1.655378e+02</td>\n",
       "      <td>1.138784e+02</td>\n",
       "      <td>1.484137e+02</td>\n",
       "      <td>9.165654e+01</td>\n",
       "      <td>1.637422e+02</td>\n",
       "      <td>1.024166e+02</td>\n",
       "      <td>1.447549e+02</td>\n",
       "      <td>8.789713e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000283709_at</th>\n",
       "      <td>3.041718e+03</td>\n",
       "      <td>1.151604e+03</td>\n",
       "      <td>1.381067e+03</td>\n",
       "      <td>1.096155e+03</td>\n",
       "      <td>2.148398e+03</td>\n",
       "      <td>1.115699e+03</td>\n",
       "      <td>2.788099e+03</td>\n",
       "      <td>2.187012e+03</td>\n",
       "      <td>3.344754e+03</td>\n",
       "      <td>7.448832e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000283849_at</th>\n",
       "      <td>2.890351e+02</td>\n",
       "      <td>3.560663e+02</td>\n",
       "      <td>6.446045e+02</td>\n",
       "      <td>1.935944e+02</td>\n",
       "      <td>3.061132e+02</td>\n",
       "      <td>3.034385e+02</td>\n",
       "      <td>7.604475e+02</td>\n",
       "      <td>3.200346e+02</td>\n",
       "      <td>3.955641e+02</td>\n",
       "      <td>2.428535e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000283945_at</th>\n",
       "      <td>9.493886e+01</td>\n",
       "      <td>9.785038e+01</td>\n",
       "      <td>2.240519e+02</td>\n",
       "      <td>9.643774e+01</td>\n",
       "      <td>1.104331e+02</td>\n",
       "      <td>8.595035e+01</td>\n",
       "      <td>1.511579e+02</td>\n",
       "      <td>1.077721e+02</td>\n",
       "      <td>8.132073e+01</td>\n",
       "      <td>9.463355e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000284048_at</th>\n",
       "      <td>4.678409e+02</td>\n",
       "      <td>3.686980e+02</td>\n",
       "      <td>2.543581e+02</td>\n",
       "      <td>4.222234e+02</td>\n",
       "      <td>4.232427e+02</td>\n",
       "      <td>3.789874e+02</td>\n",
       "      <td>6.760300e+02</td>\n",
       "      <td>6.044093e+02</td>\n",
       "      <td>3.608101e+02</td>\n",
       "      <td>4.633948e+02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000284309_at</th>\n",
       "      <td>8.648453e+01</td>\n",
       "      <td>1.246421e+02</td>\n",
       "      <td>2.044919e+02</td>\n",
       "      <td>5.592258e+01</td>\n",
       "      <td>1.238702e+02</td>\n",
       "      <td>7.474300e+01</td>\n",
       "      <td>1.037059e+02</td>\n",
       "      <td>4.628900e+01</td>\n",
       "      <td>7.587696e+01</td>\n",
       "      <td>7.634999e+01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ENSG00000284543_at</th>\n",
       "      <td>3.672677e+02</td>\n",
       "      <td>4.656970e+02</td>\n",
       "      <td>3.431775e+02</td>\n",
       "      <td>4.719511e+02</td>\n",
       "      <td>3.554314e+02</td>\n",
       "      <td>2.433046e+02</td>\n",
       "      <td>7.185735e+02</td>\n",
       "      <td>6.962862e+02</td>\n",
       "      <td>3.399668e+02</td>\n",
       "      <td>2.908867e+02</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>17912 rows × 10 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                               GSM4045109    GSM4045110    GSM4045111  \\\n",
       "ID                                                                      \n",
       "AFFX-BioB-3_at               1.755863e+03  1.051528e+03  7.036322e+02   \n",
       "AFFX-BioB-5_at               2.609266e+03  8.619696e+02  8.917588e+02   \n",
       "AFFX-BioB-M_at               4.659923e+03  1.701677e+03  1.386187e+03   \n",
       "AFFX-BioC-3_at               1.748921e+04  6.778294e+03  4.773245e+03   \n",
       "AFFX-BioC-5_at               1.115263e+04  4.549913e+03  4.474977e+03   \n",
       "AFFX-BioDn-3_at              1.796681e+05  1.122930e+05  4.220047e+04   \n",
       "AFFX-BioDn-5_at              4.038222e+04  1.115087e+04  6.377619e+03   \n",
       "AFFX-CreX-3_at               5.466199e+05  3.840433e+05  1.072299e+05   \n",
       "AFFX-CreX-5_at               4.124788e+05  2.596821e+05  8.421221e+04   \n",
       "AFFX-DapX-3_at               3.894212e+01  7.236191e+01  8.733181e+01   \n",
       "AFFX-DapX-5_at               5.563402e+01  4.068950e+01  8.341774e+01   \n",
       "AFFX-DapX-M_at               3.460741e+01  5.899745e+01  7.992320e+01   \n",
       "AFFX-HSAC07/X00351_3_at      6.868457e+05  6.909729e+05  2.234569e+05   \n",
       "AFFX-HSAC07/X00351_5_at      1.972463e+05  1.142630e+05  2.374328e+04   \n",
       "AFFX-HSAC07/X00351_M_at      5.489923e+05  3.414072e+05  1.088369e+05   \n",
       "AFFX-hum_alu_at              1.854373e+06  1.912195e+06  1.016447e+06   \n",
       "AFFX-HUMGAPDH/M33197_3_at    2.832526e+05  4.096226e+05  1.442499e+05   \n",
       "AFFX-HUMGAPDH/M33197_5_at    2.191365e+05  1.986953e+05  2.883444e+04   \n",
       "AFFX-HUMGAPDH/M33197_M_at    2.384620e+05  3.097419e+05  6.115301e+04   \n",
       "AFFX-HUMISGF3A/M97935_3_at   7.371359e+04  2.724134e+04  5.598092e+03   \n",
       "AFFX-HUMISGF3A/M97935_5_at   8.081984e+02  1.294272e+02  1.072945e+02   \n",
       "AFFX-HUMISGF3A/M97935_MA_at  8.839185e+03  2.402806e+03  1.264187e+03   \n",
       "AFFX-HUMISGF3A/M97935_MB_at  5.896802e+03  1.122953e+03  1.785512e+02   \n",
       "AFFX-HUMRGE/M10098_3_at      7.909970e+03  1.136161e+04  1.458287e+04   \n",
       "AFFX-HUMRGE/M10098_5_at      3.932404e+03  6.275596e+03  7.927674e+03   \n",
       "AFFX-HUMRGE/M10098_M_at      7.568390e+03  7.466982e+03  9.892887e+03   \n",
       "AFFX-LysX-3_at               3.531883e+01  3.673993e+01  4.246824e+01   \n",
       "AFFX-LysX-5_at               4.490146e+01  3.093758e+01  4.479816e+01   \n",
       "AFFX-LysX-M_at               4.842260e+01  8.224320e+01  1.276286e+02   \n",
       "AFFX-M27830_3_at             4.255318e+02  1.193517e+03  3.570117e+03   \n",
       "...                                   ...           ...           ...   \n",
       "LINC00836                    8.380857e+01  1.171674e+02  2.542338e+02   \n",
       "ST3GAL4-AS1                  3.021504e+02  3.673940e+02  2.919499e+02   \n",
       "CTBP1-AS                     1.411848e+02  1.356484e+02  2.217986e+02   \n",
       "LINC01395                    6.671617e+01  6.898182e+01  6.493662e+01   \n",
       "TRG-AS1                      1.622814e+03  5.904574e+02  6.321255e+02   \n",
       "LINC01127                    1.193389e+02  2.513251e+02  2.205077e+02   \n",
       "GHET1                        5.111353e+01  1.094283e+02  1.196598e+02   \n",
       "LINC00934                    7.726465e+01  1.649858e+02  1.789765e+02   \n",
       "LINC01097                    7.354629e+01  4.954148e+01  9.637506e+01   \n",
       "LINC00950                    1.284265e+02  1.817042e+02  3.036536e+02   \n",
       "LINC00997                    1.014409e+02  1.755433e+02  2.978431e+02   \n",
       "ARRDC3-AS1                   3.878131e+02  5.748631e+02  6.368871e+02   \n",
       "RASSF1-AS1                   2.749528e+02  3.360092e+02  2.906803e+02   \n",
       "EBLN3P                       2.748961e+04  9.031401e+03  3.571447e+03   \n",
       "PACRG-AS1                    1.570721e+02  1.580482e+02  3.487350e+02   \n",
       "LINC01012                    5.440292e+01  7.351251e+01  7.917156e+01   \n",
       "LINC00550                    2.346779e+01  2.164096e+01  2.760505e+01   \n",
       "HCP5B                        4.053197e+02  5.272324e+02  3.382034e+02   \n",
       "LINC01144                    2.636523e+02  2.293225e+02  6.287470e+02   \n",
       "TRBV25-1                     2.768496e+01  2.618768e+01  4.219478e+01   \n",
       "FRG1CP                       4.471846e+03  3.079122e+02  2.020928e+03   \n",
       "KLF18                        7.235463e+01  8.309179e+01  7.866811e+01   \n",
       "OR5AK4P                      2.037513e+02  4.324295e+02  8.130921e+02   \n",
       "ENSG00000283703_at           1.258596e+02  1.301257e+02  1.655378e+02   \n",
       "ENSG00000283709_at           3.041718e+03  1.151604e+03  1.381067e+03   \n",
       "ENSG00000283849_at           2.890351e+02  3.560663e+02  6.446045e+02   \n",
       "ENSG00000283945_at           9.493886e+01  9.785038e+01  2.240519e+02   \n",
       "ENSG00000284048_at           4.678409e+02  3.686980e+02  2.543581e+02   \n",
       "ENSG00000284309_at           8.648453e+01  1.246421e+02  2.044919e+02   \n",
       "ENSG00000284543_at           3.672677e+02  4.656970e+02  3.431775e+02   \n",
       "\n",
       "                               GSM4045112    GSM4045113    GSM4045114  \\\n",
       "ID                                                                      \n",
       "AFFX-BioB-3_at               2.308084e+03  1.456057e+03  2.987627e+03   \n",
       "AFFX-BioB-5_at               2.243988e+03  1.252745e+03  3.113805e+03   \n",
       "AFFX-BioB-M_at               5.372558e+03  2.825406e+03  7.320880e+03   \n",
       "AFFX-BioC-3_at               1.627430e+04  1.169582e+04  2.147305e+04   \n",
       "AFFX-BioC-5_at               1.135881e+04  6.828429e+03  1.362722e+04   \n",
       "AFFX-BioDn-3_at              1.690839e+05  1.070336e+05  1.551901e+05   \n",
       "AFFX-BioDn-5_at              3.466787e+04  2.023786e+04  3.971513e+04   \n",
       "AFFX-CreX-3_at               5.520122e+05  4.616768e+05  7.120973e+05   \n",
       "AFFX-CreX-5_at               3.595671e+05  2.780945e+05  4.919018e+05   \n",
       "AFFX-DapX-3_at               3.849554e+01  2.586933e+01  4.976531e+01   \n",
       "AFFX-DapX-5_at               3.350288e+01  4.898914e+01  6.775167e+01   \n",
       "AFFX-DapX-M_at               2.986146e+01  4.488523e+01  4.943990e+01   \n",
       "AFFX-HSAC07/X00351_3_at      7.430455e+05  5.791595e+05  8.414095e+05   \n",
       "AFFX-HSAC07/X00351_5_at      1.878236e+05  2.002396e+05  2.407423e+05   \n",
       "AFFX-HSAC07/X00351_M_at      4.707339e+05  4.900337e+05  5.827385e+05   \n",
       "AFFX-hum_alu_at              1.798335e+06  1.705037e+06  1.821483e+06   \n",
       "AFFX-HUMGAPDH/M33197_3_at    4.352737e+05  3.411160e+05  4.181495e+05   \n",
       "AFFX-HUMGAPDH/M33197_5_at    2.113432e+05  3.011332e+05  3.958054e+05   \n",
       "AFFX-HUMGAPDH/M33197_M_at    3.013173e+05  3.327942e+05  3.666560e+05   \n",
       "AFFX-HUMISGF3A/M97935_3_at   1.268083e+04  3.452911e+04  3.035638e+04   \n",
       "AFFX-HUMISGF3A/M97935_5_at   1.599489e+02  2.876874e+02  2.012268e+02   \n",
       "AFFX-HUMISGF3A/M97935_MA_at  3.286319e+03  2.453882e+03  2.828798e+03   \n",
       "AFFX-HUMISGF3A/M97935_MB_at  1.081362e+03  1.461913e+03  1.595176e+03   \n",
       "AFFX-HUMRGE/M10098_3_at      4.819461e+04  1.324270e+04  9.364781e+03   \n",
       "AFFX-HUMRGE/M10098_5_at      5.173239e+04  2.823140e+04  8.260244e+03   \n",
       "AFFX-HUMRGE/M10098_M_at      4.004570e+04  1.751118e+04  7.960958e+03   \n",
       "AFFX-LysX-3_at               2.662290e+01  4.417314e+01  3.453204e+01   \n",
       "AFFX-LysX-5_at               2.658205e+01  2.818668e+01  2.602906e+01   \n",
       "AFFX-LysX-M_at               5.954139e+01  5.006925e+01  5.757026e+01   \n",
       "AFFX-M27830_3_at             8.155367e+02  9.297030e+02  6.674073e+02   \n",
       "...                                   ...           ...           ...   \n",
       "LINC00836                    1.058770e+02  1.165537e+02  6.586334e+01   \n",
       "ST3GAL4-AS1                  3.745727e+02  2.941575e+02  3.599727e+02   \n",
       "CTBP1-AS                     8.892724e+01  1.692691e+02  1.177977e+02   \n",
       "LINC01395                    6.443267e+01  7.558109e+01  6.001126e+01   \n",
       "TRG-AS1                      7.132672e+02  8.574431e+02  6.427795e+02   \n",
       "LINC01127                    3.255506e+02  2.400394e+02  3.352030e+02   \n",
       "GHET1                        5.356148e+01  6.643359e+01  4.924642e+01   \n",
       "LINC00934                    1.385062e+02  1.435644e+02  8.145322e+01   \n",
       "LINC01097                    6.446172e+01  4.992021e+01  4.358246e+01   \n",
       "LINC00950                    1.616215e+02  1.684381e+02  9.930234e+01   \n",
       "LINC00997                    1.794031e+02  1.295527e+02  1.159935e+02   \n",
       "ARRDC3-AS1                   4.753206e+02  3.937129e+02  5.105110e+02   \n",
       "RASSF1-AS1                   2.355413e+02  2.587016e+02  3.664831e+02   \n",
       "EBLN3P                       9.166557e+03  1.153876e+04  1.137597e+04   \n",
       "PACRG-AS1                    1.636432e+02  1.667425e+02  1.833777e+02   \n",
       "LINC01012                    6.873824e+01  6.511249e+01  5.469167e+01   \n",
       "LINC00550                    2.510187e+01  2.568066e+01  2.470717e+01   \n",
       "HCP5B                        3.078281e+02  4.898737e+02  3.062724e+02   \n",
       "LINC01144                    2.069933e+02  3.496224e+02  1.883269e+02   \n",
       "TRBV25-1                     2.795604e+01  3.153416e+01  2.809673e+01   \n",
       "FRG1CP                       2.423757e+03  2.926161e+02  1.428656e+03   \n",
       "KLF18                        7.715398e+01  8.868531e+01  6.613909e+01   \n",
       "OR5AK4P                      2.029329e+02  4.001370e+02  2.494575e+02   \n",
       "ENSG00000283703_at           1.138784e+02  1.484137e+02  9.165654e+01   \n",
       "ENSG00000283709_at           1.096155e+03  2.148398e+03  1.115699e+03   \n",
       "ENSG00000283849_at           1.935944e+02  3.061132e+02  3.034385e+02   \n",
       "ENSG00000283945_at           9.643774e+01  1.104331e+02  8.595035e+01   \n",
       "ENSG00000284048_at           4.222234e+02  4.232427e+02  3.789874e+02   \n",
       "ENSG00000284309_at           5.592258e+01  1.238702e+02  7.474300e+01   \n",
       "ENSG00000284543_at           4.719511e+02  3.554314e+02  2.433046e+02   \n",
       "\n",
       "                               GSM4045115    GSM4045116    GSM4045117  \\\n",
       "ID                                                                      \n",
       "AFFX-BioB-3_at               8.619126e+03  6.851476e+04  2.395435e+03   \n",
       "AFFX-BioB-5_at               1.375395e+04  6.001064e+04  1.530273e+03   \n",
       "AFFX-BioB-M_at               2.139660e+04  1.254495e+05  3.307275e+03   \n",
       "AFFX-BioC-3_at               6.747849e+04  2.500523e+05  1.359552e+04   \n",
       "AFFX-BioC-5_at               4.363743e+04  2.163762e+05  7.453435e+03   \n",
       "AFFX-BioDn-3_at              3.844489e+05  9.922842e+05  1.374475e+05   \n",
       "AFFX-BioDn-5_at              9.817101e+04  3.929779e+05  2.371066e+04   \n",
       "AFFX-CreX-3_at               9.597436e+05  1.637867e+06  4.925552e+05   \n",
       "AFFX-CreX-5_at               7.818489e+05  1.210629e+06  3.394657e+05   \n",
       "AFFX-DapX-3_at               1.373165e+02  1.157588e+02  4.061084e+01   \n",
       "AFFX-DapX-5_at               3.004492e+02  9.462634e+01  4.003301e+01   \n",
       "AFFX-DapX-M_at               1.000536e+02  2.600284e+02  5.734094e+01   \n",
       "AFFX-HSAC07/X00351_3_at      5.643952e+05  6.761790e+05  6.886985e+05   \n",
       "AFFX-HSAC07/X00351_5_at      3.061958e+04  3.730134e+04  2.391718e+05   \n",
       "AFFX-HSAC07/X00351_M_at      1.091917e+05  1.522655e+05  5.596867e+05   \n",
       "AFFX-hum_alu_at              2.187894e+06  1.744950e+06  1.694161e+06   \n",
       "AFFX-HUMGAPDH/M33197_3_at    1.848463e+05  4.208204e+05  3.889034e+05   \n",
       "AFFX-HUMGAPDH/M33197_5_at    5.206185e+04  1.480541e+05  3.724460e+05   \n",
       "AFFX-HUMGAPDH/M33197_M_at    6.934988e+04  1.995295e+05  3.846219e+05   \n",
       "AFFX-HUMISGF3A/M97935_3_at   1.364868e+04  2.129259e+04  2.659678e+04   \n",
       "AFFX-HUMISGF3A/M97935_5_at   1.460646e+02  1.435098e+02  2.556011e+02   \n",
       "AFFX-HUMISGF3A/M97935_MA_at  2.598615e+03  1.249116e+03  2.621227e+03   \n",
       "AFFX-HUMISGF3A/M97935_MB_at  3.685668e+02  2.415570e+02  9.368665e+02   \n",
       "AFFX-HUMRGE/M10098_3_at      1.168455e+04  5.652781e+04  5.963767e+03   \n",
       "AFFX-HUMRGE/M10098_5_at      4.612189e+03  1.063473e+05  8.587409e+03   \n",
       "AFFX-HUMRGE/M10098_M_at      6.481459e+03  7.755317e+04  5.898283e+03   \n",
       "AFFX-LysX-3_at               8.051537e+01  2.834344e+02  3.385307e+01   \n",
       "AFFX-LysX-5_at               6.342960e+01  3.432736e+02  4.189544e+01   \n",
       "AFFX-LysX-M_at               3.259435e+02  1.890808e+02  3.887226e+01   \n",
       "AFFX-M27830_3_at             1.290183e+03  8.238710e+02  5.888021e+02   \n",
       "...                                   ...           ...           ...   \n",
       "LINC00836                    1.878555e+02  6.795693e+01  6.966192e+01   \n",
       "ST3GAL4-AS1                  5.035231e+02  3.875506e+02  5.655795e+02   \n",
       "CTBP1-AS                     1.936232e+02  2.193928e+02  1.901629e+02   \n",
       "LINC01395                    7.382139e+01  1.316112e+02  7.458588e+01   \n",
       "TRG-AS1                      7.423100e+02  1.398641e+03  1.008531e+03   \n",
       "LINC01127                    3.112343e+02  3.041061e+02  4.955021e+02   \n",
       "GHET1                        3.476788e+02  7.425843e+01  5.627091e+01   \n",
       "LINC00934                    1.765650e+02  8.070117e+01  1.088027e+02   \n",
       "LINC01097                    1.408929e+02  6.608350e+01  5.188158e+01   \n",
       "LINC00950                    2.376496e+02  1.634580e+02  1.338300e+02   \n",
       "LINC00997                    1.167505e+02  1.881942e+02  1.147452e+02   \n",
       "ARRDC3-AS1                   9.479642e+02  1.143480e+03  4.719819e+02   \n",
       "RASSF1-AS1                   5.789443e+02  5.439730e+02  3.129780e+02   \n",
       "EBLN3P                       3.367037e+03  5.405570e+03  7.310212e+03   \n",
       "PACRG-AS1                    1.734486e+02  2.016184e+02  1.551759e+02   \n",
       "LINC01012                    1.268777e+02  6.798058e+01  5.485846e+01   \n",
       "LINC00550                    6.144764e+01  4.501257e+01  2.911259e+01   \n",
       "HCP5B                        7.101475e+02  4.502677e+02  4.449688e+02   \n",
       "LINC01144                    5.226923e+02  4.543992e+02  3.743490e+02   \n",
       "TRBV25-1                     4.009371e+01  4.174284e+01  2.713000e+01   \n",
       "FRG1CP                       6.994452e+02  1.330983e+03  1.619610e+03   \n",
       "KLF18                        1.543208e+02  9.700119e+01  6.998682e+01   \n",
       "OR5AK4P                      9.473338e+02  4.334772e+02  3.020590e+02   \n",
       "ENSG00000283703_at           1.637422e+02  1.024166e+02  1.447549e+02   \n",
       "ENSG00000283709_at           2.788099e+03  2.187012e+03  3.344754e+03   \n",
       "ENSG00000283849_at           7.604475e+02  3.200346e+02  3.955641e+02   \n",
       "ENSG00000283945_at           1.511579e+02  1.077721e+02  8.132073e+01   \n",
       "ENSG00000284048_at           6.760300e+02  6.044093e+02  3.608101e+02   \n",
       "ENSG00000284309_at           1.037059e+02  4.628900e+01  7.587696e+01   \n",
       "ENSG00000284543_at           7.185735e+02  6.962862e+02  3.399668e+02   \n",
       "\n",
       "                               GSM4045118  \n",
       "ID                                         \n",
       "AFFX-BioB-3_at               1.549348e+03  \n",
       "AFFX-BioB-5_at               1.574032e+03  \n",
       "AFFX-BioB-M_at               4.248116e+03  \n",
       "AFFX-BioC-3_at               1.416617e+04  \n",
       "AFFX-BioC-5_at               7.641976e+03  \n",
       "AFFX-BioDn-3_at              1.055391e+05  \n",
       "AFFX-BioDn-5_at              2.417201e+04  \n",
       "AFFX-CreX-3_at               5.121528e+05  \n",
       "AFFX-CreX-5_at               3.521837e+05  \n",
       "AFFX-DapX-3_at               5.164075e+01  \n",
       "AFFX-DapX-5_at               3.785649e+01  \n",
       "AFFX-DapX-M_at               5.963054e+01  \n",
       "AFFX-HSAC07/X00351_3_at      6.887205e+05  \n",
       "AFFX-HSAC07/X00351_5_at      2.343083e+05  \n",
       "AFFX-HSAC07/X00351_M_at      5.519344e+05  \n",
       "AFFX-hum_alu_at              1.671716e+06  \n",
       "AFFX-HUMGAPDH/M33197_3_at    3.487891e+05  \n",
       "AFFX-HUMGAPDH/M33197_5_at    3.086704e+05  \n",
       "AFFX-HUMGAPDH/M33197_M_at    3.026603e+05  \n",
       "AFFX-HUMISGF3A/M97935_3_at   2.164598e+04  \n",
       "AFFX-HUMISGF3A/M97935_5_at   2.162182e+02  \n",
       "AFFX-HUMISGF3A/M97935_MA_at  2.865892e+03  \n",
       "AFFX-HUMISGF3A/M97935_MB_at  1.259107e+03  \n",
       "AFFX-HUMRGE/M10098_3_at      2.299509e+04  \n",
       "AFFX-HUMRGE/M10098_5_at      1.340800e+04  \n",
       "AFFX-HUMRGE/M10098_M_at      1.210365e+04  \n",
       "AFFX-LysX-3_at               3.061428e+01  \n",
       "AFFX-LysX-5_at               3.094531e+01  \n",
       "AFFX-LysX-M_at               5.385793e+01  \n",
       "AFFX-M27830_3_at             9.541505e+02  \n",
       "...                                   ...  \n",
       "LINC00836                    8.563582e+01  \n",
       "ST3GAL4-AS1                  2.765174e+02  \n",
       "CTBP1-AS                     8.401229e+01  \n",
       "LINC01395                    5.880468e+01  \n",
       "TRG-AS1                      1.458032e+03  \n",
       "LINC01127                    1.641224e+02  \n",
       "GHET1                        6.438532e+01  \n",
       "LINC00934                    8.909109e+01  \n",
       "LINC01097                    5.197344e+01  \n",
       "LINC00950                    1.421620e+02  \n",
       "LINC00997                    1.332840e+02  \n",
       "ARRDC3-AS1                   5.338657e+02  \n",
       "RASSF1-AS1                   2.358641e+02  \n",
       "EBLN3P                       1.836648e+04  \n",
       "PACRG-AS1                    1.641504e+02  \n",
       "LINC01012                    6.461353e+01  \n",
       "LINC00550                    2.196796e+01  \n",
       "HCP5B                        2.450065e+02  \n",
       "LINC01144                    2.386898e+02  \n",
       "TRBV25-1                     2.952858e+01  \n",
       "FRG1CP                       2.675468e+03  \n",
       "KLF18                        6.855877e+01  \n",
       "OR5AK4P                      3.134657e+02  \n",
       "ENSG00000283703_at           8.789713e+01  \n",
       "ENSG00000283709_at           7.448832e+02  \n",
       "ENSG00000283849_at           2.428535e+02  \n",
       "ENSG00000283945_at           9.463355e+01  \n",
       "ENSG00000284048_at           4.633948e+02  \n",
       "ENSG00000284309_at           7.634999e+01  \n",
       "ENSG00000284543_at           2.908867e+02  \n",
       "\n",
       "[17912 rows x 10 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "g.head(10).T"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import GEOparse\n",
    "\n",
    "dataset = GEOparse.get_GEO('GSE136400', destdir='./test/data')\n",
    "\n",
    "type(dataset)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "print()\n",
    "print(\"GSM example:\")\n",
    "for gsm_name, gsm in dataset.gsms.items():\n",
    "    print(\"Name: \", gsm_name)\n",
    "    print(\"Metadata:\",)\n",
    "    for key, value in gsm.metadata.items():\n",
    "        print(\" - %s : %s\" % (key, \", \".join(value)))\n",
    "    print (\"Table data:\",)\n",
    "    print (gsm.table.shape)\n",
    "    break"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "print()\n",
    "print(\"GPL example:\")\n",
    "for gpl_name, gpl in dataset.gpls.items():\n",
    "    print(\"Name: \", gpl_name)\n",
    "    print(\"Metadata:\",)\n",
    "    for key, value in gpl.metadata.items():\n",
    "        print(\" - %s : %s\" % (key, \", \".join(value)))\n",
    "    print(\"Table data:\",)\n",
    "    print(gpl.table.head())\n",
    "    break"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "platforms = {}\n",
    "\n",
    "for gpl_name, gpl in dataset.gpls.items():\n",
    "    platforms[gpl_name] = gpl.table\n",
    "\n",
    "for k, v in platforms.items():\n",
    "    print(k, v.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "metadata = {'ID': []}\n",
    "\n",
    "for gsm_name, gsm in dataset.gsms.items():\n",
    "    \n",
    "    metadata['ID'].append(gsm_name)\n",
    "    \n",
    "    for key, value in gsm.metadata.items():\n",
    "        \n",
    "        if key != 'characteristics_ch1':\n",
    "            \n",
    "            if key not in metadata:\n",
    "                metadata[key] = []\n",
    "                \n",
    "            metadata[key].append(', '.join(value))            \n",
    "\n",
    "metadata = pd.DataFrame(metadata).set_index('ID')\n",
    "\n",
    "metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "\n",
    "result, keys = {}, set()\n",
    "\n",
    "for gsm_name, gsm in dataset.gsms.items():\n",
    "    \n",
    "    for item in gsm.metadata['characteristics_ch1']:\n",
    "        \n",
    "        k, _ = item.split(': ')\n",
    "        \n",
    "        keys.add(k)\n",
    "\n",
    "for gsm_name, gsm in dataset.gsms.items():\n",
    "    \n",
    "    local_keys = set()\n",
    "    \n",
    "    for item in gsm.metadata['characteristics_ch1']:\n",
    "        \n",
    "        k, v = item.split(': ')\n",
    "        \n",
    "        local_keys.add(k)\n",
    "        \n",
    "        if k not in result:\n",
    "            result[k] = []\n",
    "        result[k].append(v if v != '--' else None)\n",
    "    \n",
    "    for k in keys.difference(local_keys):\n",
    "        result[k].append(None)\n",
    "\n",
    "pd.DataFrame(result).head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "platform.iloc[:8, :6]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "r = None\n",
    "\n",
    "for gsm_name, gsm in dataset.gsms.items():\n",
    "    \n",
    "    # platform_id = gsm.metadata['platform_id'][0]\n",
    "    \n",
    "    # platform = platforms[platform_id]\n",
    "    \n",
    "    # ttt = platform.merge(tmp[['ID_REF']], left_on='ID', right_on='ID_REF')\n",
    "    \n",
    "    tmp = gsm.table[['ID_REF', 'VALUE']].set_index('ID_REF')\n",
    "    \n",
    "    tmp.columns = [gsm_name]\n",
    "    \n",
    "    if r is None:\n",
    "        r = tmp\n",
    "    else:\n",
    "        r = r.join(tmp, how='left')\n",
    "    \n",
    "r.iloc[:8, :8]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import GEOparse\n",
    "import pandas as pd\n",
    "\n",
    "def load_data_from_geo(geo_id, dst_path='.', silent=True):\n",
    "    \"\"\"\n",
    "\n",
    "    :param geo_id:\n",
    "    :param dst_path:\n",
    "    :param silent:\n",
    "    :return:\n",
    "    \"\"\"\n",
    "\n",
    "    dataset = GEOparse.get_GEO(geo_id, destdir=dst_path, silent=silent)\n",
    "\n",
    "    # Parsing platforms\n",
    "    platforms = {}\n",
    "    for gpl_name, gpl in dataset.gpls.items():\n",
    "        platforms[str(gpl_name).upper()] = gpl.table\n",
    "        \n",
    "    # loading keys\n",
    "    keys, metadata_keys = set(), set()\n",
    "    for gsm_name, gsm in dataset.gsms.items():\n",
    "        \n",
    "        # gettin all characteristics key\n",
    "        for item in gsm.metadata['characteristics_ch1']:\n",
    "            k, _ = item.strip().split(': ', 1)\n",
    "            k = k.lower().strip().replace(' ', '_').replace('/', '_')\n",
    "            keys.add(k)\n",
    "        \n",
    "        # getting all metadata keys\n",
    "        for key, value in gsm.metadata.items():\n",
    "            k = key.lower().strip().replace(' ', '_').replace('/', '_')\n",
    "            if key != 'characteristics_ch1':\n",
    "                metadata_keys.add(k)\n",
    "\n",
    "    # parsing metadata, characteristics, and genes\n",
    "    metadata, genes, characteristics = {'ID': [], **{c: [] for c in metadata_keys}}, None, {'ID': [], **{c: [] for c in keys}}\n",
    "    \n",
    "    for gsm_name, gsm in dataset.gsms.items():\n",
    "        \n",
    "        # metadata\n",
    "        metadata_local_keys = set()\n",
    "        metadata['ID'].append(gsm_name)\n",
    "        \n",
    "        for key, value in gsm.metadata.items():\n",
    "            \n",
    "            if key != 'characteristics_ch1':\n",
    "                \n",
    "                key = key.lower().strip().replace(' ', '_').replace('/', '_')\n",
    "                \n",
    "                if key not in metadata_local_keys:\n",
    "                    metadata[key].append(', '.join(value))\n",
    "                    metadata_local_keys.add(key)\n",
    "\n",
    "        for k in metadata_keys.difference(metadata_local_keys):\n",
    "            metadata[k].append(None)\n",
    "\n",
    "        if gsm.table.shape[0] > 0:\n",
    "\n",
    "            tmp = gsm.table[['ID_REF', 'VALUE']].set_index('ID_REF')\n",
    "\n",
    "            tmp.columns = [str(gsm_name).upper()]\n",
    "            if genes is None:\n",
    "                genes = tmp\n",
    "            else:\n",
    "                genes = genes.join(tmp, how='left')\n",
    "\n",
    "        # characteristics\n",
    "        local_keys = set()\n",
    "        characteristics['ID'].append(gsm_name)\n",
    "\n",
    "        for item in gsm.metadata['characteristics_ch1']:\n",
    "\n",
    "            k, v = item.split(': ', 1)\n",
    "            \n",
    "            k = k.lower().strip().replace(' ', '_').replace('/', '_')\n",
    "            \n",
    "            if k not in local_keys:\n",
    "                local_keys.add(k)\n",
    "                characteristics[k].append(v if v != '--' else None)\n",
    "\n",
    "        for k in keys.difference(local_keys):\n",
    "            characteristics[k].append(None)\n",
    "        \n",
    "    metadata = pd.DataFrame(metadata).set_index('ID')    \n",
    "    characteristics = pd.DataFrame(characteristics).set_index('ID')\n",
    "\n",
    "    if genes is not None:\n",
    "        genes = genes.reset_index().rename(columns={'ID_REF': 'ID'}).set_index('ID')\n",
    "        genes = genes.T\n",
    "\n",
    "    return characteristics, genes, metadata, platforms\n",
    "\n",
    "characteristics, genes, metadata, platforms = load_data_from_geo('GSE136400', dst_path='./test/data')\n",
    "\n",
    "characteristics.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "\n",
    "df = characteristics.copy()\n",
    "\n",
    "delete = ['eventid', 'imidgiven', 'time_btwn', 'sampleprotocol', 'gepprocesslocation', \n",
    "          'ftprotocol', 'ftprotocolbase', 'datepulled', 'datelastcontact', 'sampledatetime', 'sampledatetime__1',\n",
    "          'iss1', 'iss2', 'iss3', 'protocolsample', 'celfilernbx', 'datapulled', 'sampleid', 'chipdate', 'sampleprotocol.1',\n",
    "          'datebasesample', 'dateenrolled', 'datesample', 'cell_type', 'protocol_fill', 'inregimenstep', 'datechip', 'location.signal',\n",
    "          'datesamplernbx', 'descname', 'celfilernas', 'agelte65', 'refchip', 'celname', 'wide_pointgoup', 'wide_pointgroup', 'point',\n",
    "          'pc_bmbxtxt', 'issr', 'sorting', 'wide_include', 'tissue', 'censorforosdate', 'censorforpfsdate', 'sampletype', 'processed_site',\n",
    "          'chiptype', 'tc', 'fnpatid', 'transplant', 'isexpress', 'censos.ar', 'censpfs.ar', 'agelte75', 'hyperdiploidclinicalfish',\n",
    "          'amp1qclinicalfish', 'del13qclinicalfish', 'del16qclinicalfish', 'del17pclinicalfish', 't_11_14clinicalfish', 't_4_14clinicalfish',\n",
    "          'monthspfs.ar', 'uams.cd1', 'uams.cd2', 'uams.hy', 'uams.lb', 'uams.mf', 'uams.ms', 'uams.pr', 'monthsos.ar', 'monthspfs.ar2',\n",
    "          'datelastresponse', 'maxpfs', 'monthsobs', 'monthsos', 'responselast', 'imidpostresponse', 'imid_date', 'imidimproved', 'pfsgt18',\n",
    "          'maxpfsgt18mon', 'maxpfsgt24mon', 'maxpfsgt36mon'\n",
    "         ]\n",
    "\n",
    "for c in delete:\n",
    "    del df[c]\n",
    "\n",
    "df = df.replace({'FALSE': 0, 'TRUE': 1, 'NA': None, \n",
    "                 '.': None, np.nan: None, 'Not Evaluable': None, \n",
    "                 'PR_Unconfirmed': 'PR', 'NULL': None, 'Refused': None})\n",
    "\n",
    "\n",
    "def from_to_imids(x):\n",
    "    try:\n",
    "        return 'revlimid' if x.lower().startswith('revlimid') else 'thalidomide'\n",
    "    except:\n",
    "        return None\n",
    "\n",
    "\n",
    "df['imids'] = df['imids'].apply(from_to_imids)\n",
    "\n",
    "df['iss'] = df['iss'].apply(lambda x: {'I': 1, 'II': 2, 'III': 3}.get(x, None))\n",
    "\n",
    "df['gender'] = df['gender'].apply(lambda x: {'Female': 1, 'Male': 0}.get(x))\n",
    "\n",
    "# df['vital_status'] = df['datedeath'].isnull()\n",
    "del df['datedeath']\n",
    "\n",
    "df = df[df['race'].apply(lambda x: 'native' not in str(x).lower())]\n",
    "race_dummies = pd.get_dummies(df['race'].str.lower().str.replace(' / ', '_').str.replace(' ', '_'), 'race')\n",
    "del df['race']\n",
    "df = pd.concat([df, race_dummies], axis=1)\n",
    "\n",
    "imids = df['imids']\n",
    "pointgroup = df['pointgroup']\n",
    "descprotocol = df['descprotocol']\n",
    "gender = df['gender']\n",
    "cluster = df['cluster']\n",
    "\n",
    "del df['imids']\n",
    "del df['pointgroup']\n",
    "del df['descprotocol']\n",
    "del df['gender']\n",
    "del df['cluster']\n",
    "\n",
    "df = df.astype(float)\n",
    "\n",
    "df['imids'] = imids\n",
    "df['pointgroup'] = pointgroup\n",
    "df['descprotocol'] = descprotocol\n",
    "df['gender'] = gender\n",
    "df['cluster'] = cluster\n",
    "\n",
    "for c in ['gender', 'ageatsampledate', 'imids', 'iss', 'ldh', 'b2m']:\n",
    "    df = df[~df[c].isnull()]\n",
    "\n",
    "for c in df.columns:\n",
    "    if df[c].isnull().sum() / df.shape[0] > .05:\n",
    "        del df[c]\n",
    "       \n",
    "df['risk_group'] = (df['monthspfs'] > df['monthspfs'].mean()).astype(float)\n",
    "del df['monthspfs']\n",
    "\n",
    "df['transplant'] = (df['numberoftransplants'] > 0).astype(int)\n",
    "del df['numberoftransplants']\n",
    "\n",
    "df = df.rename(columns={'ageatsampledate': 'age_at_diagnosis', 'imids': 'treatment'})\n",
    "\n",
    "print(df.shape)\n",
    "df.head(10).T.sort_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "for c in sorted(df.columns):\n",
    "    print(c, df[c].unique())\n",
    "    print()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "r = {'c': [], 'm': []}\n",
    "\n",
    "for c in sorted(df.columns):\n",
    "    r['c'].append(c)\n",
    "    r['m'].append(df[c].isnull().sum() / df.shape[0])\n",
    "    \n",
    "print(df.shape)\n",
    "pd.DataFrame(r).sort_values('m').set_index('c').sort_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "\n",
    "import missingno as msn\n",
    "\n",
    "msn.matrix(df[sorted(df.columns)])"
   ]
  }
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