Test for differential expression

Now that you have defined a design matrix and a contrasts matrix, you can test for differential expression due to doxorubicin treatment in the two types of mice.

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 doxorubicin data, the design matrix design, and the contrasts matrix cm have been loaded in your workspace. The limma package is already loaded.

Fit the model coefficients with lmFit.
Fit the contrasts with contrasts.fit.
Calculate the t-statistics with eBayes.
Summarize the results with decideTests and vennDiagram.

Hands-on interactive exercise

Have a go at this exercise by completing this sample code.

# 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)

# Create a Venn diagram
___(results)

Edit and Run Code