High-Throughput GoMiner Detailed Output Descriptions

A subdirectory is created within the data directory, and its name is based upon that of the total gene file. It contains two classes of objects:

  1. Several files that summarize the overall results from all of the changed gene files:

  2. A subdirectory [CHANGEDGENESFILE.dir] corresponding to each of the changed gene files (for each file type mentioned, there is one for the underexpressed, overexpressed, and changed genes if the changed gene file was of the two column format):
  3. Subdirectories for integration of all changed gene files [CHANGEALL.dir] Allows the user to determine the specific genes that are in the categories of interest, integrated across all of the changed-gene files, without needing to go back and search through a large number of individual gce files. Also permits analysis of this relationship by clustering.

Debug Information

If you used the debug option, then additional information about the execution of High-Throughput GoMiner is retained. The contents of the DEBUG file depend on the DEBUG parameter in the config file. The most reasonable setting is 2. If the setting is 1, then there is an excess of information that is probably not too useful. Only the most confident user should set 0, as then error conditions might go unnoticed.

The first thing to do after completion of a High-Throughput GoMiner run is to look a the bottom of the DEBUG file. If it says "NORMAL TERMINATION", you can be pretty sure everything went well. You might want to scroll through the whole file quickly and look for things that went to STDERR but that did not generate a problem that was picked up by the shell.

On the other hand, if there was a detectable problem, then the end of the DEBUG file is where that will be reported, since everything stops when a problem is detected. Usually, the error will be reported with an error code. You can work your way backwards (or upwards) to get some hints of where the problem specifically occurred, and either correct your dataset or config parameters, or send us a bug report.

GoMiner™ is a development of the Genomics and Pharmacology Facility, Developmental Therapeutics Branch (DTB), Center for Cancer Research (CCR), National Cancer Institute (NCI).

Please email us with any problems, questions or feedback on the tool.

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