Create an ExpressionSet object

Managing 3 different data sets for one experiment is tedious and error-prone, especially if you need to perform any filtering. Combine the 3 data sets from the leukemia experiment into a unified object using the Bioconductor class ExpressionSet.

This exercise is part of the course

Differential Expression Analysis with limma in R

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Exercise instructions

The expression matrix (x), feature data (f), and phenotype data (p) are loaded in your workspace.

Create a new ExpressionSet object using the function ExpressionSet.
Pass the expression matrix to the assayData argument.
Pass the phenotype data frame to the phenoData argument.
Pass the feature data frame to the featureData argument.

Hands-on interactive exercise

Have a go at this exercise by completing this sample code.

# Load package
library(Biobase)

# Create ExpressionSet object
eset <- ___(assayData = ___,
                      phenoData = AnnotatedDataFrame(___),
                      featureData = AnnotatedDataFrame(___))

# View the number of features (rows) and samples (columns)
dim(eset)

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