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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

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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 running 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, ___)

# Calculate the t-statistics
fit <- ___(fit)

# Summarize results
results <- ___(fit[, "___"])
summary(results)
Edit and Run Code