How do I run ArrayMiner from GeneSpring ?
    Run GeneSpring. Choose the organism you wish to study and then click the External Programs option in GeneSpring's Navigator. Open the "ArrayMiner" folder as shown in the following figure.

ArrayMiner Wrappers in GeneSpring

Three ways of running ArrayMiner from GeneSpring are available, via three options in the "ArrayMiner" sub-menu:

  • ArrayMiner: the standard ArrayMiner run. Gene expression data of the currently active GeneSpring's Gene List are sent to ArrayMiner, where they can be clustered. Upon exit, ArrayMiner sends the resulting clustering back to GeneSpring, which interprets the data as a new classification. This new classification can be given a name, and be subsequently handled in any way a GeneSpring's own classification would.
  • ArrayMiner on Classification: same as the above, except that a classification is sent by GeneSpring together with the expression data. This is useful for comparing a GeneSpring's clustering with ArrayMiner's. The classification sent is the one currently active in GeneSpring. Selecting this option without a selected classification will cause ArrayMiner to exit immediately.
  • ArrayMiner View: viewing a GeneSpring's clustering. Gene expression data and a classification are sent as above. However, ArrayMiner does not perform a clustering of its own, and does not attempt to send one back upon exit. This option is useful for visualization of a GeneSpring's classification with the intuitive and user-friendly visual interface of ArrayMiner. This option will also allow you to select a classification in the Classification Compare Window and set it as current in all the other windows, giving you the possibility to more precisely compare two clusterings.

There are three additional options in the ArrayMiner submenu:

  • Load Classification from File: lets you open a previously saved classification. You can only open gsc files. To learn how to create such a file, click here.
  • ArrayMiner Setup: lets you modify the way ArrayMiner is set up to run from GeneSpring. You normally need to invoke this option only when GeneSpring's data are stored in a location different from the default location. That situation typically arises in large GeneSpring installations with remote data shared by several users.
  • Refresh Annotations : This option will fill the ArrayMiner annotation database with the GeneSpring information about your organism allowing you to obtain the same description records in ArrayMiner as in GeneSpring. It will also fill the search engine database of ArrayMiner with the same Internet queries as in GeneSpring.

    Once ArrayMiner is running, you can perform your clustering as if the data were open from a file (see How to perform a clustering).

    Upon shutdown of ArrayMiner, the results are automatically sent back to GeneSpring if necessary, unless you are running under Windows 95/98/Me. Please check the special considerations here.

    To learn more on how to install ArrayMiner for GeneSpring on a Macintosh, click here.