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).
PCL File Format
PCL files may be used as input for the GSEA module. This is a format defined at Stanford for their CDNA expression data. More information on this format is available here.