The database generates .pcl files when data are retrieved. After clustering, a .cdt file is generated, and in addition, .gtr and .atr files may also be generated. The complete dataset without any processing can also be downloaded as an Excel file.
The pcl file is a tab-delimited pre-clustering file. The first three columns are as follows:
In addition the file must begin with the following two rows:
The remaining cells in the file contain the actual data, such that the row and column specifies to which gene and which experiment a particular piece of data corresponds. If you had modified, or created your pcl file in Excel, it would look something like this:
You should then choose Save As... from the File menu, and elect to the the file as type Text (Tab delimited), as indicated below:
In general the pcl file will contain log-transformed data, which is needed for clustering to work properly.
When you cluster a .pcl file you will generate a .cdt (clustered data table) file, which will contain the original data, but reordered, to reflect the clustering. In addition, if you clustered by genes, you will get a .gtr file (gene tree), and if you clustered by experiments you will get a .atr file (array tree). These tree file reflect the history of how the cluster was built, and can be used to contruct how the tree(s) should look.
The .gtr (gene tree) file records the order in which the genes (rows) were joined during clustering.
The .atr (array tree) file records the order in which the arrays (columns) were joined during clustering.