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)