\BOOKMARK [1][-]{section.1}{Introduction}{}
\BOOKMARK [1][-]{section.2}{Installation}{}
\BOOKMARK [2][-]{subsection.2.1}{System requirements}{section.2}
\BOOKMARK [2][-]{subsection.2.2}{Obtaining R}{section.2}
\BOOKMARK [2][-]{subsection.2.3}{Installation - Windows\(9x/NT/2000\)}{section.2}
\BOOKMARK [2][-]{subsection.2.4}{Installation - Linux/Unix}{section.2}
\BOOKMARK [1][-]{section.3}{Data and function list}{}
\BOOKMARK [1][-]{section.4}{Preparing the input files}{}
\BOOKMARK [2][-]{subsection.4.1}{Preparing the data files}{section.4}
\BOOKMARK [2][-]{subsection.4.2}{Preparing the design file}{section.4}
\BOOKMARK [2][-]{subsection.4.3}{Preparing the covariate matrix}{section.4}
\BOOKMARK [1][-]{section.5}{A quick tour of the functions}{}
\BOOKMARK [2][-]{subsection.5.1}{CAMDA kidney experiment}{section.5}
\BOOKMARK [2][-]{subsection.5.2}{An Affymetrix experiment}{section.5}
\BOOKMARK [1][-]{appendix.A}{Running R/maanova on computer cluster}{}
\BOOKMARK [2][-]{subsection.A.1}{System requirements}{appendix.A}
\BOOKMARK [2][-]{subsection.A.2}{System setup}{appendix.A}
\BOOKMARK [2][-]{subsection.A.3}{Install and test clusters in R}{appendix.A}
\BOOKMARK [1][-]{appendix.B}{Basic Algorithms}{}
\BOOKMARK [2][-]{subsection.B.1}{ANOVA model for microarray experiment}{appendix.B}
\BOOKMARK [3][-]{subsubsection.B.1.1}{Model}{subsection.B.1}
\BOOKMARK [3][-]{subsubsection.B.1.2}{Fixed model versus Mixed model}{subsection.B.1}
\BOOKMARK [2][-]{subsection.B.2}{Hypothesis tests}{appendix.B}
\BOOKMARK [3][-]{subsubsection.B.2.1}{F test in matrix notation}{subsection.B.2}
\BOOKMARK [3][-]{subsubsection.B.2.2}{Building L matrix}{subsection.B.2}
\BOOKMARK [3][-]{subsubsection.B.2.3}{Four flavors of F-tests}{subsection.B.2}
\BOOKMARK [2][-]{subsection.B.3}{Data shuffling in permutation test}{appendix.B}
\BOOKMARK [1][-]{appendix.C}{Frequently Asked Questions}{}
