# Calculating adjusted p values in python

When working with statistical analysis, it is often necessary to calculate adjusted p-values to account for multiple comparisons. In Python, there are several ways to accomplish this task. In this article, we will explore three different approaches to calculating adjusted p-values and determine which one is the most efficient.

## Approach 1: Using the statsmodels library

The statsmodels library in Python provides a convenient function called `multipletests` that can be used to calculate adjusted p-values. This function implements various methods for adjusting p-values, such as the Bonferroni correction, the Benjamini-Hochberg procedure, and the Holm-Bonferroni method.

``````import statsmodels.stats.multitest as smm

# Sample p-values
p_values = [0.01, 0.05, 0.1, 0.001]

# Calculate adjusted p-values using the Benjamini-Hochberg procedure

This approach is straightforward and requires minimal code. However, it may not be the most efficient option for large datasets or when performing multiple comparisons.

## Approach 2: Using the scipy library

The scipy library in Python provides a function called `fdrcorrection` that can be used to calculate adjusted p-values using the Benjamini-Hochberg procedure. This function is part of the `stats` module in scipy.

``````import scipy.stats as stats

# Sample p-values
p_values = [0.01, 0.05, 0.1, 0.001]

# Calculate adjusted p-values using the Benjamini-Hochberg procedure

This approach is similar to the first one but uses a different library. It is also efficient and provides the same functionality as the statsmodels library.

## Approach 3: Manual calculation

If you prefer a more manual approach, you can calculate adjusted p-values yourself using basic Python operations. This approach allows for more customization and flexibility but requires more code.

``````# Sample p-values
p_values = [0.01, 0.05, 0.1, 0.001]

# Number of comparisons
m = len(p_values)

# Calculate adjusted p-values using the Bonferroni correction
adjusted_p_values = [min(p_value * m, 1) for p_value in p_values]

This approach manually applies the Bonferroni correction to each p-value. It is the most customizable option but may not be the most efficient for large datasets or complex adjustment methods.

After evaluating the three approaches, it is clear that the first two options using the statsmodels and scipy libraries are the most efficient and convenient ways to calculate adjusted p-values in Python. These libraries provide built-in functions that implement various adjustment methods, saving time and effort for the user. However, if customization and flexibility are a priority, the manual calculation approach can be a suitable alternative.

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### 13 Responses

1. Kase Patrick says:

Approach 2 with scipy seems simpler. But hey, who needs simplicity when you can do manual calculations, right? 😅

1. Michelle Parker says:

Well, to each their own, I guess! But personally, I prefer simplicity and saving time. Why complicate things when you have a handy tool like scipy? But hey, if you enjoy manual calculations and the extra effort, more power to you! 😄

2. Harper Ingram says:

Approach 2 using scipy seems more practical, but manual calculation has its charm too! What do you think? 🧐🤔

1. Fletcher says:

I agree with you! While approach 2 using scipy may be more practical, theres something satisfying about manually calculating. Its like solving a puzzle! Both methods have their merits, so it really depends on personal preference and the specific situation.

3. Frank Schroeder says:

Approach 2 seems more convenient, but I wonder if Approach 3 gives more control. Thoughts?

4. Ayla says:

Approach 1 seems more convenient, but Approach 3 gives you that DIY satisfaction! #PythonStats

5. Neil says:

6. Teo Zimmerman says:

Approach 2 with scipy seems easier to implement. But hey, manual calculation can be fun too! 🧮🤓

7. Harley says:

Approach 3: Manual calculation sounds tedious and error-prone. Why not use the libraries? #PythonPower

8. Finnley says:

Approach 1: statsmodels is handy, but what about performance? Any thoughts on that? #datascience

9. Frederick Boyer says:

Approach 3 seems like a lot of work, but hey, who doesnt love some manual calculations? #oldschool

1. Laylah says:

Approach 3 may require some extra effort, but its worth it for accurate results. Embracing manual calculations can be a valuable exercise, building problem-solving skills and fostering a deeper understanding. Sometimes a touch of old school can leave a lasting impact. #EmbraceTheChallenge

10. Billie Bennett says:

Approach 3 seems tedious, but hey, at least it gives you a deeper understanding! 💪🏼🤓