Note: If you are using Excel to edit GenePattern files, be sure to save the file as a tab-delimited text file and supply the correct file extension. You can specify the file name in quotes to prevent Excel from appending .txt to the file name. Also, note that Excel's auto-formatting can introduce errors in gene names, as described in Zeeberg, et al (2004).
CLM File Format
The CLM file format is a tab-delimited file format that describes the samples in a zipped collection of CEL or IDAT files (used with the ExpressionFileCreator and IlluminaExpressionFileCreator modules, respectively).
Each row of the CLM format describes a CEL file in the zip file:
(CEL file name) (tab) (sample name) (tab) (class)
cat_a.CEL sample_cat_a tumor
The first column contains the CEL file name (file extension is optional).
The second column contains a sample name for the CEL file data.
The third column contains a phenotype class name for the CEL file data.