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\author{Thon de Boer}

\title{Using R with GeneSpring}

\maketitle

\copyright{2007 Agilent Technologies}

\section{Introduction}

This package contains a number of functions to facilitate the integration of R code
into the Gene Expression analysis program GeneSpring, by Agilent Technologies.
Available functions include:

\begin{itemize}
\item \texttt{GSload.int()} - Read GeneSpring experiment interpretation from file and return a GeneSpring gene expression object (GSint).
\item \texttt{GSload.intBC()} - Read GeneSpring experiment interpretation from file and return a BioConductor gene expression object (ExpressionSet).
\item \texttt{GSload.exp()} - Read GeneSpring experiment from file and return a GeneSpring gene expression object (GSint).
\item \texttt{GSload.expBC()} - Read GeneSpring experiment from file and return a BioConductor gene expression object (ExpressionSet).
\item \texttt{GSint()} - Create a GeneSpring gene expression object (GSint).
\item \texttt{GSint2BC()} - Convert a GeneSpring gene expression object (GSint) to a BioConductor gene expression object (ExpressionSet).
\item \texttt{BC2GSint()} - Convert a BioConductor gene expression object (ExpressionSet) to a GeneSpring gene expression object (GSint).
\item \texttt{GSload.genelist()} - Read a GeneSpring GeneSpring gene list from file.
\item \texttt{GSsave.genelist()} - Save a GeneSpring GeneSpring gene list to file.
\item \texttt{GSsave.exp()} - Save a GeneSpring gene expression object (GSint) to file.
\end{itemize}

Most of the functions are conversion functions that convert files in the proprietary format
of GeneSpring, into objects that can be used by generic R functions or the BioConductor packages.
The BioConductor GeneSpring library should be used in conjunction with the
GeneSpring-R integration package that will complete the incorporation of R scripts into
GeneSpring. This GeneSpring-R integration package will install some auxiliary scripts
and programs that are needed to fully and seamlessly integrate R scripts into GeneSpring.
For more information on integrating R scripts into the GeneSpring environment see the support section on
our website at www.silicongenetics.com.

\section{GeneSpring Experiments and Interpretations}
Some definitions of GeneSpring terms will help in the construction of useful scripts.
\begin{itemize}
\item \texttt{Sample} - Expression values for a single hybridization.
\item \texttt{Experiment} - Set of samples that are related to each other. (For instance, all the samples 
for a time series or drug concentration study. Each replicate will be considered a separate sample)
\item \texttt{Interpretation} - One or more representations of the same experiments. An experiment can
be represented by combining all the Time points together, be defining the experimental parameter Time
as the parameter that defines the conditions. Each experiment can have one or more interpretations.
\item \texttt{Condition} - Group of samples that have a particular parameter in common.
(For instance, all the replicates for the measurements (samples) for time 0 hours can be combined into
one condition for Time 0)
\end{itemize}

Basically, the main difference between Experiments and Interpretations is that in Experiments, the 
samples are always represented as individual samples, while in Interpretations, one or more samples
can be combined into one condition, where the expression values are represented by the mean or average
of expression values of the samples in each of the conditions. Depending on the purpose of the analysis,
either Experiments or Interpretations can be used.

See the GeneSpring-R Integration document for more information on how to select the type of expression
data to be used in the R scripts.

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