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.
Questo esercizio fa parte del corso
Differential Expression Analysis with limma in R
Istruzioni dell'esercizio
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
decideTestsandvennDiagram.
Esercizio pratico interattivo
Prova a risolvere questo esercizio completando il codice di esempio.
# 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)