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