When working with datasets, handling missing data is a common challenge faced by data scientists and analysts. Python’s popular data manipulation library, Pandas, provides numerous methods for managing missing or not-a-number (NaN) values. However, one might stumble upon an error while attempting to apply a mask to a DataFrame or a Series: “Cannot mask with non-boolean array containing NA / NaN values”. In today’s blog post, we’re diving deep into the causes of this error and examining different techniques to solve it efficiently.

Understanding the Error

To get started, let’s grasp the context in which this error occurs. The error message usually appears when trying to apply a mask or filter to a Pandas DataFrame or Series using a boolean array containing missing (NA or NaN) values. This error arises because Pandas requires boolean arrays to have no missing values when performing element-wise masking operations.

Identifying the Error

The initial step to solving this problem is pinpointing the error. Imagine we have a dataset containing information about various products, including the price and the number of items sold. Let’s say we want to filter out the products with a price greater than 50.

import pandas as pd data = {'Product': ['A', 'B', 'C', 'D'], 'Price': [25, 55, None, 65], 'Sold': [100, 150, 120, 180]} df = pd.DataFrame(data) mask = df['Price'] > 50 filtered_data = df[mask]

Executing this code will trigger the error “Cannot mask with non-boolean array containing NA / NaN values” because the ‘Price’ column contains a missing value (None).

Handling Missing Values

To address the error, we can use several methods to manage missing values in our dataset before applying the mask. Let’s explore some common techniques.

Removing Rows with Missing Values

The most straightforward method is to remove rows containing missing values using the dropna() function. Keep in mind that this approach might not be ideal if a significant amount of data is lost.

df_cleaned = df.dropna(subset=['Price']) mask = df_cleaned['Price'] > 50 filtered_data = df_cleaned[mask]

Replacing Missing Values with a Default Value

Another option is to replace missing values with a default value using the fillna() function. This approach might be useful if you can safely assume a default value for the missing data points.

default_value = 0 df_filled = df.fillna({'Price': default_value}) mask = df_filled['Price'] > 50 filtered_data = df_filled[mask]


For ordered data, you may consider using interpolation to fill missing values based on the values of other elements in the same column. Pandas provides the interpolate() function to perform this operation.

df_interpolated = df.interpolate() mask = df_interpolated['Price'] > 50 filtered_data = df_interpolated[mask]

Using Boolean Arrays with isna() or notna()

You can create a boolean array by combining the comparison operator and the isna() or notna() functions. This method allows you to include or exclude missing values directly in the mask.

mask = (df['Price'] > 50) | df['Price'].isna() filtered_data = df[mask] mask_notna = (df['Price'] > 50) & df['Price'].notna() filtered_data_notna = df[mask_notna]

In the first example, we use the | (OR) operator to include rows with missing values in the mask. In the second example, we use the & (AND) operator along with the notna() function to exclude rows with missing values from the mask.

Working with the Mask Directly

Another approach is to work with the mask directly to handle missing values before applying it to the DataFrame or Series. The fillna() function can be used to replace NaN values in the mask with either True or False.

Replacing Missing Values with True

mask = df['Price'] > 50 mask_filled = mask.fillna(True) filtered_data = df[mask_filled]

In this example, we replace missing values in the mask with True. This means that rows with missing values will be included in the filtered dataset.

Replacing Missing Values with False

mask = df['Price'] > 50 mask_filled = mask.fillna(False) filtered_data = df[mask_filled]

Alternatively, you can replace missing values in the mask with False to exclude rows with missing values from the filtered dataset.


The “Cannot mask with non-boolean array containing NA / NaN values” error occurs when applying a mask with missing values to a Pandas DataFrame or Series. To resolve this issue, you can use various techniques to handle missing values before applying the mask. These methods include removing rows with missing values, replacing missing values with a default value, using interpolation, or combining boolean arrays with the isna() or notna() functions. Additionally, you can work with the mask directly by replacing missing values using the fillna() function.

By understanding the root cause of the error and employing these strategies, you can effectively handle missing data in your datasets and avoid running into the “Cannot mask with non-boolean array containing NA / NaN values” error.

Disclaimer: The code snippets and examples provided on this blog are for educational and informational purposes only. You are free to use, modify, and distribute the code as you see fit, but I make no warranties or guarantees regarding its accuracy or suitability for any specific purpose. By using the code from this blog, you agree that I will not be held responsible for any issues or damages that may arise from its use. Always exercise caution and thoroughly test any code in your own development environment before using it in a production setting.

Leave A Comment