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, and the number of names listed must match the number of classes. If there are two classes, you need two entries.

Random Notes

Using GenePattern from within R

• Install rJava package (from CRAN)

• Install GenePattern package - from the GenePattern web client, choose Downloads -> Programming Libraries, and then the GenePattern_version.zip file. You can then use this to "install from local zip file" from within R.