Specify a linear model to compare 2 groups
To identify differentially expressed genes for the leukemia experiment, you need to translate the following linear model to R:
where \(X_{1}\) is equal to 1 for progressive cancers and 0 for stable cancers (note: R automatically chooses the base condition by alphabetical order).
Diese Übung ist Teil des Kurses
Differential Expression Analysis with limma in R
Anleitung zur Übung
The ExpressionSet object eset with the leukemia data has been loaded in your workspace.
- Use
model.matrixto construct a design matrix with an intercept coefficient and a coefficient that indicates the disease status.
Interaktive Übung
Versuche dich an dieser Übung, indem du diesen Beispielcode vervollständigst.
# Create design matrix for leukemia study
design <- ___(~___, data = ___(eset))
# Count the number of samples modeled by each coefficient
colSums(design)