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