• The About ArrayMiner 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.
• In 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 "Start on load" checkbox specifies if the algorithm should automatically start after data loading
  • the "Update Log Every" field lets you specify the refresh speed of the log window in milliseconds
  • the "Keep Log" checkbox lets you specify if you want to keep the text log between two ArrayMiner sessions
  • the "Use web help files" checkbox lets you open the help files from Optimal Design website, insuring you that you use the latest help files

Menu File

• 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 sent back to GeneSpring must match those sent to ArrayMiner.
• The Recent option lets you access the recently used files
• The Import Data option open the data importer window
• The Project Explorer option open the project explorer window
• The Load Data From Clipboard option lets you open a previously copied data set from the clipboard
• 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.
• The Run Clustering option allows you to (re)start the algorithm when it is idle. This command can be also accessed by the Apple-G shortcut.
• The Stop Clustering option allows you to stop the clustering algorithm when it is running. This command can be also accessed by the Apple-H shortcut. Note that the stopped algorithm can again be resumed with the Run clustering option.

Menu Window

• The Magnifier On/Off option shows/hides a magnifier for the graphic windows (keyboard Apple-M). 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 Open All 2ndry graphs option brings up all the secondary graphic windows.
• The Close All 2ndry graphs option close all the secondary graphic windows.
• The Main Graph option brings up the main window
• The Closest Cluster option brings up the closest cluster 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 Log Window option brings up the log 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 Install GeneSpring Wrappers option will install the ArrayMiner interface files for GeneSpring.
• 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 whether your version is up to date, or whether a newer one is available from Optimal Design.