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).
ATR File Format
ATR files will be created by the HierarchicalClustering module. This is a format defined at Stanford for their Hierarchical Clustering program. Note that the HierarchicalClustering module will also generate a CDT file.
The ATR (array tree) file records the order in which the arrays (columns) were joined during clustering.