• The Open option is used to open a file formatted in CSV. Note that this option and its associated button are not available when ArrayMiner is run from within GeneSpring, because the data are passed directly from GeneSpring and the classification sent back to GeneSpring must pertain to those data.
• The Import Data option open the data importer window.
• The Get Data From Clipboard option lets you open a previously copied data set from the clipboard.
• The Reload current option gives the possibility to restart the optimization process from the scratch on the data currently loaded in ArrayMiner. Since the algorithm used by ArrayMiner is stochastic in nature, this may yield a different suite of solutions being examined by the algorithm.
• The Save option allows you to save the solution currently available in ArrayMiner to a file or to the system clipboard (more).
• The Save As behaves the same way as the Save option but will always ask for a file name.

Menu Execution

After loading your file and initializing the population, the algorithm goes into idle mode. The following options are then accessible in the Execution menu.

• In Run Preferences, you can set the conditions that, when met, will prompt the algorithm to report that the optimization process is finished. The following two fields are available in the preferences (more on the optimization):
  • the Max age field is used to tell the algorithm to prompt the user when the solution did not improve after the given number of iterations. This is useful for detecting the moment when the algorithm can be safely stopped, as the probability of improving the solution is then small
  • the Step field allows you to automatically stop the optimization every x iterations, where x is the specified number.
• The Run clustering option allows you to (re)start the algorithm when it is idle. This command can be also accessed by the Ctrl-E shortcut.
• The Stop clustering option allows you to stop the clustering algorithm when it is running. This command can be also accessed by pressing the ESC key. Note that the stopped algorithm can again be resumed with the Run clustering option.

Menu Window

• The Graph On/Off option shows/hides the main graphic window (keyboard shortcut Ctrl-G). Note that the exact position of the window is remembered and reapplied when it is reopen.
• The 2ndary graph On/Off (keyboard shortcut Ctrl-D) option shows/hides all of the other graphic windows simultaneously. This is very useful when the desktop becomes crowded. Note that the exact position of each window is remembered and reapplied when it is reopened.
• The Open All 2ndry graphs (keyboard shortcut Ctrl-W) option brings up all the secondary graphic windows.
• The Magnifier On/Off option shows/hides a magnifier for the graphic windows (keyboard shortcut F7). This is in particular extremely useful on monitors in high-resolution modes, or when a precise positioning of the mouse pointer is necessary (e.g. when selecting a profile in the Activities window).
• The Minimize all application lets you minimize all ArrayMiner windows at once. Thanks to the keyboard shortcut (F11), only one keystroke is necessary to minimize the whole of ArrayMiner, whatever the active window.
• The Graphic Image Depth lets you specify the bit depth used for image rendering. The rendering is set to 32 bit by default, since most graphical hardware is compatible with that mode. Setting the depth to 15 bit accelerates the display (most notably for the translucent 3D hulls), and reduces the memory needed by the display. It is worth switching to the 15 bit depth to check whether your hardware is compatible with the mode.
• The Text Log Window option brings up the log window
• The Main Graph option brings up the main window
• The Closest Clusters option brings up the closest clusters window
• The Raw Data option brings up the raw data window
• The Progress option brings up the progress window
• The Classification Compare option brings up the classification compare window
• The Project Notes option brings up the project notes window
• The Information option brings up the information window
• The Search option brings up the search window
• The Experiment Tree option brings up the experiment tree window

Menu Tools

• The Get GeneSpring data order from clipboard option allows you to reorder the data sent by GeneSpring.
• The Check for update option allows you to check if your ArrayMiner version is up to date, or a newer one is available from Optimal Design.

Menu Help

• The Help option opens this help viewer.
• The Wizard option allows you to show/hide the contextual help in the Wizard Panel in the Control window.
• The Documentation option opens a folder where you can easily access all relevant documentation on ArrayMiner, including a Manual and the Release Notes for the version of ArrayMiner you are running.
• The About/Licence option brings up the Copyright box. The box also shows the version number of ArrayMiner you are running, as well as the license number you use, the expiration date of the license and the identity of the licensee. These data are valuable for checking whether an update of the license is necessary.