ANOVA also known as Analysis of Variance is a powerful statistical method to test a hypothesis involving more than two groups (also known as treatments). However, ANOVA is limited in providing a detailed insights between different treatments or groups, and this is where, Tukey (T) test also known as T-test comes in to play. In this tutorial, I will show how to prepare input files and run ANOVA and Tukey test in R software. For detailed information on ANOVA and R, please read this article at this link.

3. Finally, install the library qtl in R

# Step 1.3: Preparing the Input file

Create an input file as shown in the example below:

# Step 2: Run ANOVA in R

### 2.1 Import R package

Install R package agricolae and open the library typing the below command line:

library(agricolae)


Note: Please remember to install the correct R package for ANOVA!

### 2.2 Import data

Import your data by typing the below command line:

data= read.table(file = "fileName.txt", header = T)


### 2.3 Check data

Once the data is imported, check it by typing the below command line:

head(data_pressure)
tail(data_pressure)


### 2.4 Conduct ANOVA

Now, Simply run ANOVA by typing the below command lines:

data.lm <- lm(data$Dependent_variable ~ data$Treatment, data = data)

data.av <- aov(data.lm)
summary(data.av)


The results should look similar as seen below:

> summary(data.av)
Df Sum Sq Mean Sq F value   Pr(>F)
data$Treatment 3 139.2 46.38 38.49 1.69e-08 *** Residuals 20 24.1 1.20 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1  From the summary output, one can interpret that there is a significant difference (i.e. P < 0.001) between the Treatments, however, we perfom Tukey’s Test to investigate the differences between all treaments using steps below. ### 3.0 Conduct Tukey test Type below commands to run Tukey test: data.test <- TukeyHSD(data.av) data.test  Below is the summary of the Tukey test: > data.test Tukey multiple comparisons of means 95% family-wise confidence level Fit: aov(formula = data.lm)$data\$Treatment
B-A  2.52666667  0.7527896 4.300544 0.0037260
D-A  5.74500000  3.9711229 7.518877 0.0000001
E-A  5.72583333  3.9519563 7.499710 0.0000001
D-B  3.21833333  1.4444563 4.992210 0.0003106
E-B  3.19916667  1.4252896 4.973044 0.0003326
E-D -0.01916667 -1.7930437 1.754710 0.9999897


From the above T-test, one can conclude that there is a significant difference in the most of groups, except between-groups E-D at P <0.001

Finally, one can plot the above results using the below command:

plot(data.test)


Output:

### --- End of Tutorial ---

Thank you for reading this tutorial. If you have any questions or comments, please let me know in the comment section below or send me an email.

### Bibliography

Felipe de Mendiburu (2019). agricolae: Statistical Procedures for Agricultural Research. R package version 1.3-1. https://CRAN.R-project.org/package=agricolae