How to perform a Bonferroni Correction in R

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A one-way ANOVA is used to determine whether or not there is a statistically significant difference between the means of three or more independent groups.

If the overall p-value from the ANOVA table is less than some significance level, then we have sufficient evidence to say that at least one of the means of the groups is different from the others.

However, this doesn’t tell us which groups are different from each other. It simply tells us that not all of the group means are equal.

In order to find out exactly which groups are different from each other, we must conduct pairwise t-tests between each group while controlling for the family-wise error rate.

One of the most common ways to do so is to use Bonferroni’s correction when calculating the p-values for each of the pairwise t-tests.

This tutorial explains how to perform Bonferroni’s correction in R.

Example: Bonferroni’s Correction in R

Suppose a teacher wants to know whether or not three different studying techniques lead to different exam scores among students.

To test this, she randomly assigns 10 students to use each studying technique. After one week of using their assigned study technique, each student takes the same exam.

We can use the following steps in R to fit a one-way ANOVA and use Bonferroni’s correction to calculate pairwise differences between the exam scores of each group.

Step 1: Create the dataset.

The following code shows how to create a dataset that contains exam scores for all 30 students:

#create data frame
data <- data.frame(technique = rep(c("tech1", "tech2", "tech3"), each = 10),
                   score = c(76, 77, 77, 81, 82, 82, 83, 84, 85, 89,
                             81, 82, 83, 83, 83, 84, 87, 90, 92, 93,
                             77, 78, 79, 88, 89, 90, 91, 95, 95, 98))

#view first six rows of data frame
head(data)

  technique score
1     tech1    76
2     tech1    77
3     tech1    77
4     tech1    81
5     tech1    82
6     tech1    82

Step 2: Visualize the exam scores for each group.

The following code shows how to produce boxplots to visualize the distribution of exam scores for each group:

boxplot(score ~ technique,
        data = data,
        main = "Exam Scores by Studying Technique",
        xlab = "Studying Technique",
        ylab = "Exam Scores",
        col = "steelblue",
        border = "black")

The following code shows how to perform a one-way ANOVA to test for differences among mean exam scores in each group:

#fit the one-way ANOVA model
model <- aov(score ~ technique, data = data)

#view model output
summary(model)

            Df Sum Sq Mean Sq F value Pr(>F)  
technique    2  211.5  105.73   3.415 0.0476 *
Residuals   27  836.0   30.96                 
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Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Since the overall p-value (0.0476) is less than .05, this is an indication that each group does not have the same average exam score.

Next, we will perform pairwise t-tests using Bonferroni’s correction for the p-values to calculate pairwise differences between the exam scores of each group.

Step 4: Perform pairwise t-tests.

To perform pairwise t-tests with Bonferroni’s correction in R we can use the pairwise.t.test() function, which uses the following syntax:

pairwise.t.test(x, g, p.adjust.method=”bonferroni”)

where:

• x: A numeric vector of response values
• g: A vector that specifies the group names (e.g. studying technique)

The following code shows how to use this function for our example:

#perform pairwise t-tests with Bonferroni's correction
pairwise.t.test(data$score, data$technique, p.adjust.method="bonferroni")

	Pairwise comparisons using t tests with pooled SD 

data:  data$score and data$technique 

      tech1 tech2
tech2 0.309 -    
tech3 0.048 1.000

P value adjustment method: bonferroni

The way to interpret the output is as follows:

• The adjusted p-value for the mean difference in exam scores between technique 1 and technique 2 is .309.
• The adjusted p-value for the mean difference in exam scores between technique 1 and technique 3 is .048.
• The adjusted p-value for the mean difference in exam scores between technique 2 and technique 3 is 1.000.

Based on the output, we can see that the only significant difference is between technique 1 and technique 3.

An Introduction to the One-Way ANOVA
How to Conduct a One-Way ANOVA in R
How to Perform Tukey’s Test in R
How to Perform Dunnett’s Test in R