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\title{Lab 1: Bioconductor Basics} \bibliographystyle{plainnat}

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In this laboratory we will introduce some of the basic interactions with Bioconductor.

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library(Biobase) library(annotate) library(golubEsets)

@

The package \texttt{golubEsets} contains three data sets that were obtained from the web and slightly massaged. They represent the data analysed in \citet{Golub99} to perform class prediction using microarray data. The data were collected on Affymetrix Hu 6800 chip and which contains probes for 7129 genes.

An \texttt{exprSet} basically consists of the gene expression matrix (optionally a set of standard errors for those estimates), the related experimental metadata (who did what when and to what), and the phenotypic data. Here phenotype is interpreted quite broadly -- it represents any physical characteristics of the sample.

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data(golubTrain)

golubTrain

golubTrain[,1:10]

golubTrain[1:100,]

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Notice that when subsetting we have arranged it so that the \textit{rows} correspond to genes and the \textit{columns} correspond to samples.

The phenotypic data are stored in a separate, but linked, data frame. You can obtain it and interact with it using specific methods.

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pD <- phenoData(golubTrain)

pD

pd <- pData(pD)

pd

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An object of class \texttt{phenoData} is a combination of a dataframe containing the various data elements and a list that explains what each variable represents. This information is usually relegated to a help page but we felt that it was important to keep it more closely associated with the data.

The \verb+$+ operator performs the job of extracting particular variables from an object of class \texttt{phenoData}. It also can be used directly on the \texttt{exprSet}.

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table(pD$ALL.AML)

##different data data(golubTest) table(golubTest$ALL.AML)

@ %$ The S4 methods package has introduced substantial new capabilities into R. To obtain the manual pages for S4 classes you should use the following syntax \texttt{class?exprSet}. Please do that now and we will look at help page.

Almost all R functions have a set of runnable examples that are shown at the bottom of the manual page. You can either scroll down to them and cut-and-paste them across or use the R function \Rfunction{example} to run them. Try \texttt{example(exprSet)}.

To see what packages are currently loaded into your R session you can use \Rfunction{search}. You can list the functions in any package that is attached by using \texttt{objects("package:ts")}, for example. This will list all the objects in the time series package \Rpackage{ts}. Another useful command is \Rfunction{find} which will tell you which package contains the definition of a function.

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