Test for differential expression between 2 groups
Now that you have an ExpressionSet object and a design matrix, you can fit and test your model with limma.
This exercise is part of the course
Differential Expression Analysis with limma in R
Exercise instructions
The ExpressionSet object eset
with the leukemia data and the design matrix you just created (design
) have been loaded in your workspace.
Fit the model coefficients with
lmFit
.Calculate the t-statistics with
eBayes
.Summarize the results with
decideTests
.Since it doesn't make sense to test the intercept term, specify the coefficient
"Diseasestable"
when runningdecideTests
.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Load package
library(limma)
# Fit the model
fit <- ___(eset, ___)
# Calculate the t-statistics
fit <- ___(fit)
# Summarize results
results <- ___(fit[, "___"])
summary(results)