The raw data files are also stored in these subdirectories. The subdirectory, variable names and files for the yeast, colon cancer, leukemia , and test data analyses are given below. The datasets are representations of the expression data, including labels for each case and attribute. Each row represents a case and each column an attribute. Classes store model parameters which have been generated by AutoClass.
Categories are database representations of functional category assignments, etc.
Combined variables are generated by combining the principle variable types and are used in many of the analysis and graphing routines. The data are normalized by chip as described in the Alon paper. This data set is rotated relative to the Yeast data because we cluster patients by gene, rather than genes by patient. The test data is used to verify the code and to illustrate the methods with 'fake' data. The noise is randomly generated and added to the patterns with an std of 0.1.