(1)读取“GSE83148_series_matrix.txt”基因芯片文件和平台“GPL570-55999.txt”(跳过注释行),分别命名为df1和df2 (2)清除df1与df2中的重复数据和缺失数据(df1清除存在NaN的行,df2清除“Gene Symbol”列存在NaN的行) (3)df2新增一列“gene”其值为“Gene Symbol”列的第一个基因名,df1的“ID_REF”列重命名为“ID”列,df2保留“ID”和“gene”列然后与df1合并为df,df中gene名相同的记录表达量取平均值,打印df (4)转置df,并在后面添加一列label,以“N”标识正常样本,以“C”标识肿瘤样本,这些信息可以从“GSE83148_series_matrix.txt”基因芯片文件的“!Sample_title”行提取,打印并保存df (5)将“label”列转换为哑变量(k-1),并作为df的最后一列,删除label列 (6)任选两个基因,分别对其表达量进行离差标准化和标准差标准化(结果不需要保存到df中) (7)尝试任选一个基因,离散化其表达量(不需要保存) (8)统计df的每个基因在肿瘤和正常样本上表达量的平均值,并保存为A (9)提前A中表达量差值的绝对值最大的10个基因名¶
时间: 2023-10-08 20:11:01 浏览: 112
很好,以下是你的答案:
(1)
```python
import pandas as pd
df1 = pd.read_csv('GSE83148_series_matrix.txt', sep='\t', skiprows=79)
df2 = pd.read_csv('GPL570-55999.txt', sep='\t', skiprows=31)
```
(2)
```python
df1.dropna(inplace=True)
df2.dropna(subset=['Gene Symbol'], inplace=True)
df2['gene'] = df2['Gene Symbol'].str.split(' /// ').str[0]
df1.rename(columns={'ID_REF': 'ID'}, inplace=True)
df = pd.merge(df1, df2[['ID', 'gene']], on='ID')
df = df.groupby('gene').mean().reset_index()
```
(3)
```python
df = df.T.reset_index()
df.columns = df.iloc[0]
df = df[1:].reset_index(drop=True)
df['label'] = df['!Sample_title'].str.extract(r'(N|C)')
df = df.iloc[:, :-1]
dummy_label = pd.get_dummies(df['label'], prefix='label', drop_first=True)
df = pd.concat([df.iloc[:, :-1], dummy_label], axis=1)
df.drop('!Sample_title', axis=1, inplace=True)
```
(4)
```python
df = df.T.reset_index()
df.columns = df.iloc[0]
df = df[1:].reset_index(drop=True)
df['label'] = df['!Sample_title'].str.extract(r'(N|C)')
df = df.iloc[:, :-1]
dummy_label = pd.get_dummies(df['label'], prefix='label', drop_first=True)
df = pd.concat([df.iloc[:, :-1], dummy_label], axis=1)
df.drop('!Sample_title', axis=1, inplace=True)
```
(5)
```python
from sklearn.preprocessing import LabelEncoder, OneHotEncoder
label_encoder = LabelEncoder()
df['label'] = label_encoder.fit_transform(df['label'])
one_hot_encoder = OneHotEncoder(categories='auto', sparse=False)
dummy_label = one_hot_encoder.fit_transform(df[['label']])
dummy_label = pd.DataFrame(dummy_label, columns=['label_N', 'label_C'])
df = pd.concat([df.iloc[:, :-1], dummy_label], axis=1)
df.drop('label', axis=1, inplace=True)
```
(6)
```python
from sklearn.preprocessing import StandardScaler
# 离差标准化
scaler1 = StandardScaler()
df['gene1_normalized'] = scaler1.fit_transform(df[['gene1']])
# 标准差标准化
scaler2 = StandardScaler(with_std=False)
df['gene2_normalized'] = scaler2.fit_transform(df[['gene2']])
```
(7)
```python
# 离散化
df['gene3_discretized'] = pd.cut(df['gene3'], bins=3, labels=['low', 'medium', 'high'])
```
(8)
```python
A = df.groupby('gene').mean()[['label_N', 'label_C']]
```
(9)
```python
A['diff'] = abs(A['label_N'] - A['label_C'])
top10_genes = A.nlargest(10, 'diff').index.tolist()
```
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