python - 尝试使用 PyComBat 消除我的结果的批处理效果

Question

我正在尝试消除 2 个实验的批次效应。结果在两个 csv 文件中......

我在使用 Jupyter Notebook 的 Windows 10 上，我尝试了以下代码：

!pip install combat
!pip install combat --upgrade

from combat.pycombat import pycombat
import pandas as pd
import matplotlib.pyplot as plt


dataset_1 = pd.read_pickle("dataset1.csv")
dataset_2 = pd.read_pickle("dataset2.csv")



df_expression = pd.concat([dataset_1,dataset_2,dataset3],join="inner",axis=1)


plt.boxplot(df_expression.transpose())
plt.show()

但显示错误：

Requirement already satisfied: combat in c:\users\joans\anaconda3\lib\site-packages (0.3.0)
Requirement already satisfied: mpmath==1.1.0 in c:\users\joans\anaconda3\lib\site-packages (from combat) (1.1.0)
Requirement already satisfied: patsy==0.5.1 in c:\users\joans\anaconda3\lib\site-packages (from combat) (0.5.1)
Requirement already satisfied: pandas==1.1.5 in c:\users\joans\anaconda3\lib\site-packages (from combat) (1.1.5)
Requirement already satisfied: numpy==1.18.5 in c:\users\joans\anaconda3\lib\site-packages (from combat) (1.18.5)
Requirement already satisfied: pytz>=2017.2 in c:\users\joans\anaconda3\lib\site-packages (from pandas==1.1.5->combat) (2021.1)
Requirement already satisfied: python-dateutil>=2.7.3 in c:\users\joans\anaconda3\lib\site-packages (from pandas==1.1.5->combat) (2.8.1)
Requirement already satisfied: six in c:\users\joans\anaconda3\lib\site-packages (from patsy==0.5.1->combat) (1.15.0)
---------------------------------------------------------------------------
UnpicklingError                           Traceback (most recent call last)
<ipython-input-6-c6007de88a15> in <module>
      7 
      8 
----> 9 dataset_1 = pd.read_pickle("dataset1.csv")
     10 dataset_2 = pd.read_pickle("dataset2.csv")
     11 

~\anaconda3\lib\site-packages\pandas\io\pickle.py in read_pickle(filepath_or_buffer, compression)
    180                 # We want to silence any warnings about, e.g. moved modules.
    181                 warnings.simplefilter("ignore", Warning)
--> 182                 return pickle.load(f)
    183         except excs_to_catch:
    184             # e.g.

UnpicklingError: unpickling stack underflow

我要使用的包是这样的：https ://epigenelabs.github.io/pyComBat/

有什么建议吗？非常感谢。

标签： pythonwindowsjupyter-notebookbatch-processing