\BOOKMARK [1][-]{section.1}{Introduction}{}
\BOOKMARK [2][-]{subsection.1.1}{Motivation}{section.1}
\BOOKMARK [2][-]{subsection.1.2}{Envisage}{section.1}
\BOOKMARK [2][-]{subsection.1.3}{The Envisage Modelling Procedure}{section.1}
\BOOKMARK [1][-]{section.2}{Getting Started}{}
\BOOKMARK [2][-]{subsection.2.1}{Getting Envisage Up and Running}{section.2}
\BOOKMARK [3][-]{subsubsection.2.1.1}{Installing R and Bioconductor}{subsection.2.1}
\BOOKMARK [3][-]{subsubsection.2.1.2}{Installing Additional Required Packages in R}{subsection.2.1}
\BOOKMARK [3][-]{subsubsection.2.1.3}{Installing Envisage in R}{subsection.2.1}
\BOOKMARK [3][-]{subsubsection.2.1.4}{Installing Tcl/Tk}{subsection.2.1}
\BOOKMARK [3][-]{subsubsection.2.1.5}{\(OPTIONAL\) Installing GeneSpring-R Integration External Program Interface}{subsection.2.1}
\BOOKMARK [2][-]{subsection.2.2}{Requirements}{section.2}
\BOOKMARK [2][-]{subsection.2.3}{Data Pre-Processing}{section.2}
\BOOKMARK [1][-]{section.3}{Running Envisage}{}
\BOOKMARK [2][-]{subsection.3.1}{Initialisation of Envisage}{section.3}
\BOOKMARK [3][-]{subsubsection.3.1.1}{Initialising Envisage from Bioconductor}{subsection.3.1}
\BOOKMARK [3][-]{subsubsection.3.1.2}{Initialising Envisage from Genespring}{subsection.3.1}
\BOOKMARK [2][-]{subsection.3.2}{Envisage Graphical User Interface}{section.3}
\BOOKMARK [3][-]{subsubsection.3.2.1}{Selection of Variables Classes}{subsection.3.2}
\BOOKMARK [3][-]{subsubsection.3.2.2}{Envisage GUI Arguments}{subsection.3.2}
\BOOKMARK [2][-]{subsection.3.3}{Envisage Output}{section.3}
\BOOKMARK [1][-]{section.4}{Program Specifications}{}
\BOOKMARK [2][-]{subsection.4.1}{User Methods}{section.4}
\BOOKMARK [2][-]{subsection.4.2}{envisage\(\) Argument Definition}{section.4}
\BOOKMARK [2][-]{subsection.4.3}{envisage\(\) Argument Information}{section.4}
\BOOKMARK [2][-]{subsection.4.4}{Non-User Methods}{section.4}
\BOOKMARK [2][-]{subsection.4.5}{S3 Classes}{section.4}
\BOOKMARK [1][-]{section.5}{An Example Envisage Session}{}
\BOOKMARK [2][-]{subsection.5.1}{Using the GUI}{section.5}
\BOOKMARK [2][-]{subsection.5.2}{Using the command line}{section.5}
\BOOKMARK [2][-]{subsection.5.3}{Envisage output}{section.5}
