A group of filters applied to a given dataset is called a filter scheme. The default filter scheme consists of applying a Threshold filter, followed by a Variation filter, followed by a Normalization filter. Common Use Plan on doing several runs. Avoid using the same number for the rows and columns. Other than visually inspection, the other way to judge a clustering is to examine the error, which is printed out to a console window.
Lower error means a better clustering.
However, keep in mind that the errors are only comparable across SOM's with the same number of clusters. Thus a large SOM with a small error is not necessarily better than a smaller SOM with a higher error. But a 6x4 SOM with .68 error is always better than a 6x4 SOM with a .73 error. Inspect which genes are in which clusters by clicking in the desired cluster's box. Load these files into Excel for further analysis.