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.
Deze oefening maakt deel uit van de cursus
Differential Expression Analysis with limma in R
Oefeninstructies
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.
Praktische interactieve oefening
Probeer deze oefening eens door deze voorbeeldcode in te vullen.
# 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)