One way ANOVA in R: Difference between revisions
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* Read the file and name it (e.g metab) | * Read the file and name it (e.g metab) | ||
metab <- read.csv ("sample.csv, header= T) | metab <- read.csv ("sample.csv, header= T) | ||
* confirm the file is imported. When you call for metab and press enter you should see the table | * confirm the file is imported. When you call for metab and press enter you should see the table | ||
*make box plot | *make box plot | ||
boxplot(metab) | boxplot(metab) | ||
*Then use the following command to conduct one way anova and Tukey's test | *Then use the following command to conduct one way anova and Tukey's test | ||
smetab <- stack(metab) <br> | smetab <- stack(metab) <br> | ||
names(smetab) <- c("length", "group") <br> | names(smetab) <- c("length", "group") <br> | ||
smetab <br> | smetab <br> | ||
av1<-aov(length ~ group, data=smetab) <br> | av1<-aov(length ~ group, data=smetab) <br> | ||
summary(av1) <br> | summary(av1) <br> | ||
tk<- TukeyHSD(av1) <br> | tk<- TukeyHSD(av1) <br> | ||
tk <br> | tk <br> | ||
[[Category:Protocols]] | [[Category:Protocols]] | ||
[[Category:Metabolomics]] | [[Category:Metabolomics]] | ||
Revision as of 23:40, 11 November 2015
The one way analysis of variance is used to test if three or more means are equal. One way ANOVA is an extension of two independent samples t-test.
using R
- Open the R console
- Change the working directory to the directory where your file is"
setwd('C:/Users/yourfolder')
- Read the file: E.g the file used here is smaple.csv. The file has three groups with the following format
| Header 1 | Header 2 | Header 3 |
|---|---|---|
| a | b | c |
| d | e | f |
- Read the file and name it (e.g metab)
metab <- read.csv ("sample.csv, header= T)
- confirm the file is imported. When you call for metab and press enter you should see the table
- make box plot
boxplot(metab)
- Then use the following command to conduct one way anova and Tukey's test
smetab <- stack(metab)
names(smetab) <- c("length", "group")
smetab
av1<-aov(length ~ group, data=smetab)
summary(av1)
tk<- TukeyHSD(av1)
tk