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).
CDT File Format
CDT files are created by the HierarchicalClustering module. This is a format defined at Stanford for their Hierarchical Clustering program. The CDT (clustered data table) file contains the original data, but reordered, to reflect the clustering. Note that the HierarchicalClustering module will also generate the following files:
if you clustered by genes, a GTR file (gene tree)
if you clustered by samples, an ATR file (array tree)
These tree files reflect the history of how the cluster was built, and can be used to contruct how the tree(s) should look.