suppressPackageStartupMessages(library("Biobase"))

library("Biobase")

getClass("ExpressionSet")

The Bioconductor project provides S4 implementations for microarray data.

As a conclusion to our exercise, let's use the class introspection tools seen in section \ref{sec:introspec}

to study the \Robject{ExpressionSet} implementation available in the \Rpackage{Biobase} package.

<<bioenv, echo=FALSE>>=

<<biob>>=

There are of course many more slots, to support description of the

experiment itself as well as the microarray platform.

The expression data itself is stored in the \Robject{assayData} slot

that is of class \Robject{AssayData}. In practice, this generally

equates to an environment that contains one or multiple expression matrices.

The feature and sample annotations are stored in the \Robject{featureData}

and \Robject{phenoData} slots, both of class \Robject{AnnotatedDataFrame}.

An \Robject{AnnotatedDataFrame} is a \Robject{data.frame} that supports

additional variable names annotation. Each of these classes can in turn be

inspected with \Rfunction{getClass} or, better, by reading the respective documentation.

We also see that the \Robject{ExpressionSet} class extends the \Robject{eSet}

class, i.e. \Robject{ExpressionSet} is a sub-class of the \Robject{eSet} class.

See the \Robject{contains} field in \Rfunction{?setClass} to read more about

class sub/super-class extensions.