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).
CEL File Format
Affymetrix image analysis software generates CEL files, which store information about the probes on a chip and the intensity values for the probes. GenePattern modules, such as ExpressionFileCreator and SNPFileCreator, take CEL files as input and generate data files that can be read by subsequent GenePattern modules. More information on this format is available here.