X and Y size

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X and Y size

Postby MultiD Support » Thu Jul 03, 2008 9:43 am

How do I decide the X and Y sizes of the SOM?

For expression profiling there is really no reason to use SOM's of other shapes than squared. A good size of the square is using a side equal to the number of subjects classified. In GenEx this is the number of active rows, which is indicated in the information bar in the bottom. Hence, for a data set with 15 active rows a good SOM size is 15 x 15. This is also the size set by genEx per default. If the number of rows is very large GenEx default will be lower. This is because a large SOM will atke longer time to train, particular if real-time view is activated.

If you have large data sets try them in a small SOM first. If it looks promising increase the default settings and let GenEx work on it for whatever time it takes. OBS! For training of large maps deactivate the real-time view to increase speed.

MultiD Support
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