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© 2002-2005 by
Chih Long Liu

Frequently Asked Questions

Q: I use a scoring system that is a quantitative or semi-quantitative, continuous range system (i.e. not discrete numerals). How do I use the TMA-Deconvoluter to handle the score conversion? (2-23-05)

A: Version 1.10 and later of the TMA-Deconvoluter can handle continuous range scoring systems. You can find more information on how this is handled here, and the walkthroughs have been updated accordingly. If you wish to keep your scores unconverted, turn off the Score Conversion Utility (see below).

Q: How do I turn off the Score Conversion Utility when running the Deconvoluter in the default automatic mode? (4-5-03)

A: There are two options for doing this.

Option 1

  1. Select "Run Deconvoluter manually" option
  2. Click on "Run Deconvoluter". Note that this will NOT convert scores NOR output files.
  3. Click on "Output files". The files will now have been output WITHOUT having used the Score Conversion Utility.
Option 2

Download Version 1.07 (or higher) of the TMA-Deconvoluter. After selecting all your options and settings, clear all fields in the Score Conversion Utility. You can now run the Deconvoluter in automatic mode with the Score Conversion Utility off. A message dialog box will pop up after deconvolution to confirm that you want the Score Conversion Utility off.

Q: Why do the case numbers appear offset by one in the output file?

A: Your lookup file may have an offset in your case numbers. The TMA-Deconvoluter expects that for given case number n, the row on which it is found is n + 1. For example, if the case identifier is "134", TMA-Deconvoluter expects to find it on row 135. TMA-Deconvoluter also expects the first case identifier to be "1", and versions 1.04 or later will alert you to any errors in your lookup file format.

Q: Why do I get the error: "Runtime error 1004: Cannot rename a sheet to the same name as another sheet, a reference object library, or a workbook referenced by Visual Basic"?

A: You didn't properly reset the TMA-Deconvoluter after your previous use of Deconvoluter. Click "End" to dismiss the dialog box, then go back and reset the Deconvoluter. To do this, click on the "Reset" button in the Control worksheet. The TMA-Deconvoluter needs to be reset after each batch is processed so that it can clean up after itself and prevent errors like these from occurring.

Q: Are there plans for a Macintosh version of the TMA Deconvoluter or any of the other components of the TMA data management system?

A: The short answer: Yes, but on a limited basis, and not very soon (unless someone is willing to give me a Mac with Excel installed).

The long answer: The TMA data management system has been optimized for Windows-based systems, primarily because of the availability of Active X controls on the Windows platform and because the TreeView and Cluster programs are currently available only for Windows operating systems. Because of ongoing requests, a Macintosh-compatible version of the TMA Deconvoluter is currently under development and is meant to only serve as pre-processing of data for users who will eventually view the data on a Windows-based system. This Macintosh-compatible version will have a more limited user interface and features, and it will not be updated as frequently due to the author's limited accessibility to a Macintosh computer. Java-based programs that possess the capabilities of TreeView and Cluster are currently under development by the Stanford Genome Databases Group.

Update (6-26-02): The Java version of TreeView is now available here. Please note that this is a work in progress, so documentation is sparse, and not all features are implemented. You will need to install the Java Runtime Environment in order for the program to work. Please refer to the program website (at the link above) for further details, and please direct questions about this program to the program's author, Alok Saldanha.

Update (2-3-05): There haven't been any requests for a Mac version that I have heard of within the past 2 years, so currently all development efforts for the Mac have been halted. This is again mainly due to the fact that I don't own a Mac, and since we provide the TMA programs free of charge, I am unlikely to spend the time and effort to make a Mac version unless someone wishes to donate a Mac with Excel installed, for this purpose. If there are any of you who must absolutely have a Mac version, feel free to contact me.

Last edited by Chih Long Liu on November 18, 2008 anno Domini