Tissue Microarray
TMA Home
TMA Combiner
System Requirements
System requirements for deploying the TMA data management system
Explore
Explore the demonstration dataset
Download
Download the programs and documentation
Revision History
FAQ
Frequently Asked Questions
Links
Site Index
Authors
Web Portal

© 2002-2007 by
Chih Long Liu

Walkthrough TMA-Deconvoluter - 1

What you will need for this walkthrough:

Note: if this is your first time using this TMA data management system, it is recommended that you proceed to the Downloads section and download the Demo Suite files. The examples presented in this walkthrough employ those files, and you should obtain the same results in using these files and with the other necessary programs available elsewhere.
  • Raw scoring worksheets containing your TMA data
  • A lookup file containing information about each case
  • The TMA-Deconvoluter
  • The Cluster program
  • The TreeView program
  • Microsoft Excel for Windows with Visual Basic support installed
  • A Windows PC

Begin by storing a copy of the TMA-Deconvoluter, your raw scoring worksheets, and the lookup file in the same folder. (If you decide to put the files elsewhere, you will need to know how to specify the appropriate path information in the entry fields for those files).

Note that Office XP, 2003, and later usually defaults the security level to "high". In that situation, you may get this dialog box:

Macros are disabled...

To fix this, go to the Tools menu, select Macros, and then select Security, as shown below.

Select Menu

You will get this dialog box:

Select Security Level

Please ensure that "Medium" is selected. If you have "High" or "Very High" selected, the TMA-Deconvoluter will not run. Once you've clicked "OK", you may now open the TMA-Deconvoluter. A dialog box might pop up before the TMA-Deconvoluter opens, asking you if you want to enable macros (as shown below). Click "Enable Macros". If you leave them disabled, the TMA-Deconvoluter will not run.

Enable Macros

Enable Macros

After opening the TMA-Deconvoluter, you should be greeted with the screen below:

TMA-Deconvoluter 1.10 Screenshot

TMA-Deconvoluter Screenshot

Click
on the image for a larger view of the picture.

Excel normally sets the current working directory based on your default settings, which may not necessarily be the directory containing the TMA-Deconvoluter and the other files that you placed in that folder. Click on "Set Working Directory" to set the working directory to be the container for your TMA files.

Set Working Directory

Set Working Directory

You now need to specify the name of the "paraffin" lookup file. Enter the full exact filename, including the extension. (The version available for download comes prepared for operation with the demo files.)

Enter Filenames

Enter Filenames

Specify the names of your raw scoring workbooks. The TMA-Deconvoluter is capable of batch operation, so you can process multiple files at a time. A helpful feature is file list generation, where instead of having to type in all the file names of the list of files you wish to process, you can graphically select the desired files in your folder. To do this, click on "Generate filelist". An Open file dialog box will appear below:

Open dialog box

Open dialog box

Click
on the image for a larger view of the picture.

Select files by clicking and dragging. To select multiple files that are not listed next to each other, hold down the Ctrl key while selecting the desired files, either with the mouse or by using the arrow keys and the spacebar. Click "Open" to add those files to your list.

Optional: You may specify the names of the output files, which will be in text tab-delimited format. Specify the names of the output files (without the .txt extension) in the appropriate cells (see below).

Output Filenames

Output Filenames

The next step of the walkthrough will further describe the "Processed" and "Output worksheet" cells.

Option Selection

Option Selection

Choose an output option. For clustering, the default is shown above. The next step in this walkthrough will also show what the output will look like if you had chosen the K-M output option.

Score Conversion

Score Conversion

In order for TMA data to be visualized correctly under TreeView, scores need to be converted from the user's scoring system to a system compatible with TreeView. The user's scoring system can consist of discrete integers, such as that shown in the default Score Key shown above.

Version 1.07 and higher supports conversion of up to 999 discrete, user-defined scores. An example of a scoring system with more than 4 scores is shown below:

Note: the color key shown in the first column above is only shown as a guideline. It isn't necessary to indicate the above color key as depicted above; specifying the numbers will be enough, and furthermore, it won't be necessary to match your scoring system to the color key above.

Since Version 1.10, the TMA-Deconvoluter can also handle scoring systems that consist of a continuous range of scores, which can be integers or floating point decimals. In order for the TMA-Deconvoluter to convert such scores correctly, check the option below:

You will notice that the Score Key will change to appear as follows below:

Enter the minimum (usually 100% negative stain) and maximum (usually 100% positive stain) possible values for your scoring system under "Before Conversion". Also, enter the value your scoring uses to denote equivocal/uninterpretable stains. This needs to be a single value - it cannot encompass a range. Scores will be converted, by default, to a range of -2 to 2, centered at 0 (for equivocal/uninterpretable scores). You can adjust this range (listed under "After"), so long as the absolute value of the minimum and maximum converted values are equal to each other. For a more detailed discussion on how this conversion process is performed, click here.

Score conversion can be carried out separately under manual operation, but you will need to select the "Run Deconvoluter manually" option and Run Deconvoluter first before converting the scores.

Run the Deconvoluter

Run Deconvoluter

You are now ready to run the Deconvoluter. Click on the button as shown above.

back to top

Step 2 - the output files

Return to the walkthrough overview page.


Last edited by Chih Long Liu on January 17, 2007