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Test for differential expression for 3 groups

Now that you've specified the design matrix and the contrasts matrix, you can test for differential expression.

Cet exercice fait partie du cours

Differential Expression Analysis with limma in R

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Instructions

The ExpressionSet object eset with the hypoxia 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.

Exercice interactif pratique

Essayez cet exercice en complétant cet exemple de 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)
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