Design matrix for 3 groups
In the hypoxia experiment, stem cells were exposed to 3 different levels of oxygen: 1%, 5%, and 21%. To contrast the cellular function in these 3 different environments, use the group-means parametrization to specify a linear model with a coefficient for each level of oxygen.
Deze oefening maakt deel uit van de cursus
Differential Expression Analysis with limma in R
Oefeninstructies
The ExpressionSet object eset with the hypoxia data has been loaded in your workspace.
- Use
model.matrixto create a design matrix with no intercept. Recall that the variable of interest for this study (3 oxygen levels) is in the columnoxygenof the phenotype data frame.
Praktische interactieve oefening
Probeer deze oefening eens door deze voorbeeldcode in te vullen.
# Create design matrix with no intercept
design <- ___(~___ + ___, data = ___(eset))
# Count the number of samples modeled by each coefficient
colSums(design)