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.

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Differential Expression Analysis with limma in R

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The ExpressionSet object eset with the hypoxia data has been loaded in your workspace.

Use model.matrix to create a design matrix with no intercept. Recall that the variable of interest for this study (3 oxygen levels) is in the column oxygen of the phenotype data frame.

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# Create design matrix with no intercept
design <- ___(~___ + ___, data = ___(eset))

# Count the number of samples modeled by each coefficient
colSums(design)

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