• 2.1 File - database, file access operations
• 2.2 Samples - select lists of hybridized sample conditions
• 2.3 Edit - edit gene and condition subsets, E.G.L. and preferences
• 2.4 Analysis - primary analysis menus
     2.4.1 GeneClass - select gene subset for gene class data Filter
     2.4.2 Normalization - select gene intensity normalization mode
     2.4.3 Filter - select data filters to compute gene subset of interest
     2.4.4 Plot - pseudoarray image, scatter, histograms, expression profile popup plots
     2.4.5 Cluster - perform cluster analysis on data filtered genes
     2.4.6 Report - generate popup spreadsheet reports of genes and samples
  
• 2.5 View - setup genomic gene data views preferences
• 2.6 Plugins - add and execute new MAEPlugin methods
• 2.7 Help - popup documentation on MAExplorer and specific database

Menu notation

In the following menus, selections that are sub-menus are indicated by a ''. Selections prefaced with a '' and indicate '' indicate that the command is a checkbox that is enabled and disabled respectively. Checkbox menu items have a "[CB]" at the end of the command. Selections prefaced with a '' and indicate '' indicate that the command is a multiple choice "radio button" that is enabled and disabled respectively, and that only one member of the group is allowed to be on at a time. Radio button menu items have a "[RB]" at the end of the command. The default values set for an initial database are shown in the menus. Selections prefaced with a '#' indicate that the commands are available only when MAExplorer is run in the stand-alone mode. Selections prefaced with a '*' commands requires access to the backend Web server [Future]. Selections that are not currently available will be grayed out in the menus of the running program.

The following Sections 2.1 through 2.7 describe the pull-down menus in detail.