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.
Deze oefening maakt deel uit van de cursus
Differential Expression Analysis with limma in R
Oefeninstructies
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 runningdecideTests.
Praktische interactieve oefening
Probeer deze oefening eens door deze voorbeeldcode in te vullen.
# Load package
library(limma)
# Fit the model
fit <- ___(eset, ___)
# Calculate the t-statistics
fit <- ___(fit)
# Summarize results
results <- ___(fit[, "___"])
summary(results)