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Example CLS file:
{{{
35 2 1
# ALL AML
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1
}}}
The first line has the number_of_samples followed by the number_of_classes, and the number 1 (I don't know why). The second line starts with a pound sign followed by the names of the classes. This is not a comment line! The names of the classes must be unique and represent each class of samples. If there are two classes, you need two entries.


== Random Notes ==
=== Using GenePattern from within R ===
 * Install rJava package (from CRAN)
 * Install GenePattern - from the GenePattern web client, choose '''Downloads''' -> '''Programming Libraries''', and then the GenePattern_version.zip