Pandas: Replace NaN value in a cell by mean of column

Updated: February 23, 2024 By: Guest Contributor Post a comment


Handling missing data is a critical step in data preprocessing, especially when dealing with real-world datasets. In the realm of Python data manipulation, Pandas is a powerhouse library that provides robust methods for cleaning and preparing data for analysis. One common operation in data handling is replacing missing values (NaNs) with the mean of their respective column. This method of imputation helps maintain the distribution of data, making datasets more reliable for statistical analyses and machine learning models.

Throughout this tutorial, we’ll explore several approaches to replacing NaN values in a DataFrame with the mean of their respective columns. We’ll start with basic techniques and gradually move towards more advanced scenarios.

Setting Up Your Environment

First, ensure that you have Pandas installed in your Python environment:

pip install pandas

Let’s also import pandas and numpy for handling NaN values:

import pandas as pd
import numpy as np

Creating a Sample DataFrame

df = pd.DataFrame({
    'A': [1, 2, np.nan, 4],
    'B': [5, np.nan, 7, 8],
    'C': [9, 10, 11, np.nan]

This DataFrame consists of three columns with some NaN values distributed across them.

Basic Replacement Technique

The simplest way to replace NaN values with the mean of their respective columns is to use the fillna() method combined with the mean() method.

df.fillna(df.mean(), inplace=True)

This code snippet replaces all NaN values in the DataFrame with the mean of their respective columns. The inplace=True parameter modifies the original DataFrame.

Column-Specific Replacement

There may be scenarios where you’d want to replace NaN values in specific columns. For this, you can use the fillna() method on the specified column.

df['B'].fillna(df['B'].mean(), inplace=True)

This replaces NaN values in column B with the mean of B only.

Advanced Techniques

For more complex scenarios, such as when different columns might need different treatments or when you want to compute the mean without including outliers, you can apply custom logic using lambda functions or the apply() method.

Here’s an example where we replace NaN values with the mean of the column, excluding outliers using the Z-score method:

from scipy.stats import zscore

df['A'] = df['A'].transform(lambda x: x.fillna(x[abs(zscore(x)) < 3].mean()))

In this example, NaN values in column A are replaced with the mean of A, excluding values considered outliers based on their Z-score.

Dealing with Group-Specific Means

Sometimes, it makes more sense to replace NaN values with the mean calculated within certain groups. For instance, if your DataFrame includes categorical data that divides it into groups.

df['group'] = ['G1', 'G1', 'G2', 'G2']

# Calculate mean within groups and replace NaN
for name, group in df.groupby('group'):
    df.loc[df['group'] == name] = group.fillna(group.mean())

This segment shows how to replace NaN values with the mean calculated within the specific groups defined in the ‘group’ column.

Handling NaNs with Conditional Logic

In cases where replacement logic might depend on conditions, such as data points being above or below a certain value, the np.where() function provides a powerful tool.

df['A'] = np.where(pd.isnull(df['A']), 0, df['A'])

This example replaces NaN values in column A with 0, which may be suitable for specific analytical needs where mean replacement is not desired.


Replacing NaN values with the mean of their respective columns is a common and effective data imputation technique that helps maintain the integrity of datasets for analysis. Pandas provides multiple ways to achieve this, from simple column-wide to more complex, conditionally-driven replacements. Understanding and applying these methods appropriately can significantly improve the quality of your data preprocessing step, ensuring more reliable and robust analyses.