Test for differential expression for 2x2 factorial
Even though you have more contrasts than in the past examples, testing for differential expression with limma still uses the same pipeline.
This exercise is part of the course
Differential Expression Analysis with limma in R
Exercise instructions
The ExpressionSet object eset with the Populus data, the design matrix (design), and the contrasts matrix (cm) have been loaded in your workspace.
Fit the model coefficients with
lmFit.Fit the contrasts with
contrasts.fit.Calculate the t-statistics with
eBayes.Summarize the results with
decideTests.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Load package
library(limma)
# Fit the model
fit <- ___(eset, ___)
# Fit the contrasts
fit2 <- ___(fit, contrasts = ___)
# Calculate the t-statistics for the contrasts
fit2 <- ___(fit2)
# Summarize results
results <- ___(fit2)
summary(results)