Home
MADAM
Spotfinder
MIDAS
MeV
AMP
Utilities
FAQ
Formats
Contributors
Contact Us

TM4 FAQ

General Questions
MADAM Questions
Spotfinder Questions
MIDAS Questions
MeV Questions
AMP Questions

General Questions

Q. Where do I get the TM4 Software?

A. The TM4 CD, which we hand out at seminars, the website, the FTP site or another user. TM4 is open-source, free software and you are free to copy and re-distribute it.

Q. What is the .mev file format?

A. A MultiExperimentViewer, or mev, file is a tab-delimited text file that contains coordinate and expression data for a single microarray experiment. Complete details for this format are available in the mev file format specification.

Q. What license are we using?

A. The Artistic License.

Q. I cannot run Madam/MeV/Midas. When I try to run the programs, a black window opens and closes very quickly. Nothing else happens.

A. You need to install the Java Runtime Environment (JRE) on your system. If it is already installed, you may need to download and install a newer version (MIDAS requires v1.4.1 or later). Download the JRE from the Java download page or find the file "j2re-1_4_1_05-windows-i586.exe" in the "Java" directory on your TM4 CD. Run the installer and follow the prompts. For a simple installation, accept the defaults that are presented. Make a note of the directory in which the JVM is located, such as "C:\Program Files\JavaSoft\JRE\1.3.1\". Computers running Macintosh OSX or a Linux distribution should already have Java installed.

Some applications, such as parts of TIGR MeV, will require extra libraries such as Java3D (J3D). To get the J3D 1.3.1 installer, go to the Java3D download page and select Java 1.3.1 API Download. Follow the prompts and be sure to choose an OpenGL, JRE runtime, such as Java 3D for Windows (OpenGL Version) Runtime for the JRE. The Windows installer is also found in the "Java" directory on your TM4 CD (java3d-1_3_1-windows-i586-opengl-rt.exe). Run the installer and follow the prompts. When prompted for a directory, make sure to select the directory where the JVM has been installed. This is important for the J3D libraries to be recognized. If you installed the JVM to the suggested directory (for example):C:\Program Files\JavaSoft\JRE\1.3.1\ make sure it is selected as the install directory for the J3D installation.

Q. Even after I install Java, I get the same error: a black window opens and closes very quickly.

A. If you are using Windows, the problem may be with your classpath settings. Instructions for setting your classpath for use with Java can be found on this page within the Sun website.

Q. Do you offer training courses?

A. Short Course on Gene Microarray Development and Analysis: Approaches to Heart, Lung, Blood and Sleep Disorders Offered April 17-22 and again November 6-11. 16 participants.
Organizers: John Quackenbush, Ph.D., and Norman Lee, Ph.D., The Institute for Genomic Research; Gary Churchill, Ph.D., Martin Ringwald, Ph.D., and John B. Macauley, Ph.D., The Jackson Laboratory
This workshop provides intensive hands-on training in the preparation and analysis of gene chips. The focus of this workshop is on microarray approaches to the study of heart, lung, and blood disease and associated sleep disorders.
Advances in Genome Technology and BioinformaticsOctober 8 - November 5, 2003. Woods Hole, MA
Directors: Claire M. Fraser - The Institute for Genomic Research and Mitchell L. Sogin - The Marine Biological Laboratory at Woods Hole.

MADAM Questions

Q. I cannot change the reserved memory for MySql DBMS. I removed MySql with "Add/Remove Programs" from the control panel but couldn't change the amount of reserved memory after I reinstalled.

A. You might need to manually delete the "mysql" folder and its contents before you re-install MySql. If MySql is still running, you will not be able to delete the folder. Refer to the next section for instructions on halting MySql.

Q. I failed to install TIGR Madam and MySql once. Now when I try to re-install the programs it always fails.

A. MySql may already be running and preventing you from starting it again. Follow these steps to shut MySql down.
1) Open the Windows Task Manager by right-clicking the window menu bar and selecting "Task Manager...". You can also do this by pressing the "Ctrl", "Alt", and "Delete" keys simultaneously, and clicking the "Task Manager" button (Windows 2000).
2) Click the "Processes" tab and select "mysql-max.exe" in the "image name" column.
3) Click the "End Process" button;
4) Click the "OK" button to kill MySql.

Q. I cannot login the database. When I run Madam and try to login a database, I see the error message "Unable to connect to server".

A. There are two possible causes:
1) You may have mistyped your user-id or password. Please note that the user-id and password are case sensitive.
2) Your database may be incorrectly set up. Use the following steps to check it.
    a. Leave the error message showing. This will ensure that MySql is running.
    b. Open a DOS window and change the directory to "c:\mysql\bin" by typing "cd mysql\bin".
    c. Type "mysql" and hit "Return".
    d. Type "show databases".

If your database is not on the list, you need to add it to MySql.

Q. When I start the program, the dialog-requiring user ID and password appeared. I filled both fields with -root- but an error message comes back saying:

MySQL running. Madam connect: access denied for user

A. The userid "root" and its password "root" should work. If not, you may have to log into the server as root and check the mysql.user table.
In directory c:\mysql\bin start the mysql command line, prompt with

1) 'mysql -p -u root'. Type 'root' as your password. (If that does not work, try using no password.)
2) use mysql;
3) select * from user;

If the entries for root have no password, you should set one:

4) update user set password = password ("whateveryoulike") where user like 'root%';

If the root entries already have a password, try resetting it using the command above.
Lastly, create a user for yourself, so that you do not have to use root:

5) grant ALL on db.* to 'userid@localhost'; grant ALL on db.* to 'userid';

Q. I am not able to change the user id and password.

A. Try the following:
Save the following commands as a script called root_set.sql

GRANT ALL ON *.* to root@localhost identified by 'root'; GRANT select, insert, update, delete, shutdown ON mage.* to root@localhost identified by 'root'; GRANT select, insert, update, delete, shutdown ON test_mage.* to root@localhost identified by 'root'; GRANT ALL ON *.* to root@"%" identified by 'root'; GRANT select, insert, update, delete, shutdown ON mage.* to root@'%' identified by 'root'; GRANT select, insert, update, delete, shutdown ON test_mage.* to root identified by 'root';
First, open the file and change all the "root" before @ to your own user name and 'root' after by to his password.
Then, save the file. To run the script, you have to launch MySql with this command:
"mysqld-max --datadir=C:/mysql/data --language=C:/mysql/share/english'
after moving the cursor to the mysql\bin folder.
Then open another DOS window and move the cursor to mysql\bin.
Type "root_set.sql" at the mysql prompt.

Q. I get the following error. It looks like my database was not created properly. What should I do? null MySql started Madam.connect: General error: Unknown database 'mage' Unable to connect to server.

A.Suggested options:
1) completely remove and reinstall madam and mysql, making certain to extract archive to a directory having a path with no spaces.
2) check c:\mysql\innodb for files; if not there, innodb tables were not created. Edit my.cnf and start mysql standalone
3) if innodb tables exist, start the server and 'use' mage or test_mage. If these dbs are not there, create them with the scripts of the same name.

Instructions to create mage and test_mage databases:
1) Exit the mysql command prompt, but leave the mysql server running.
2) Use the following commands at the DOS command line:

cd c:\mysql mysql < mage.sql > mysql < test_mage.sql >
These commands are based on the assumption that the data files 'mage.sql' and 'test_mage.sql' are located in the mysql directory. If they are located in a different directory on your machine, then include that path prepended to your filename, e.g.

mysql < c:\mypath\mage.sql > mysql < c:\mypath\test_mage.sql >

Spotfinder Questions

Q. Why are there no gene identifiers in Spotfinder output tav files?

A. To keep them in the most concise format, TAV files generated by Spotfinder do not include annotation information for each gene. This information is stored either in annotation files or databases, and can be retrieved and attached Spotfinder-generated TAVs.

Q. After aligning the grids, when I click the process all button I got an error message "exception in processall grids".

A. First of all check that your image is real 16 bit grays scale image and not 8 bit. It has to be written in correct pixel scaling mode, i.e. spot pixels have high values readings and background pixels have low readings. If not, it means that the image was inverted by scanning software. Make sure that you saved image without LZW compression.

MIDAS Questions

Q. Can MIDAS be launched on OS other than Windows?

A. Yes, MIDAS is written in Java and thus platform-independent. The latest release of MIDAS v2.18 has been tested on a variety of platforms including Windows2000, WindowsXP, Linux7.2, MacOS10.2.

Q. Can MIDAS process microarray data in formats other than TIGR-tav and TIGR-mev formats?

A. Currently MIDAS can only process TIGR-tav and TIGR-mev data formats. However, our ExpressConverter, which is also available for free download, can convert several other data formats to TIGR-tav or TIGR-mev format. Please visit our Utilities web page for further information about ExpressConverter.

Q. Should SD regularization be applied before LOWESS nomalization or after it?

A. We suggest normalizing the data with Lowess and then regularizing the SD. This is because intensity dependent effects could skew the SD for some data. Lowess should remove this and make the data more comparable.

Q. Could you please explain the importance of SD regularization?

A. Block mode SD regularization (or variance regularization) is a process that tries to compensate for areas of the array that are noisier than others. It, like most of the other approaches, assumes that the array is randomly constructed so that the genes in one pen group are no more likely than any other to be highly differentially expressed. Slide mode SD regularization does the same thing, although between slides. Since you don't have to make such assumptions here, SD regularization tries to make the variance the same across slides. This can help with between-slide comparisons.

MeV Questions

Q. I am trying to run TMEV in Linux. I have Java installed, but when I try to run the program, I get this error:

Failed to load Main-Class manifest attribute from TMEV.jar

A. Execute this command from the MEV root directory:


								java -Xmx512m -cp "TMEV.jar:Lib/algorithms.jar

								:Lib/algorithms-gui.jar:Lib/algorithms-impl.jar

								:Lib/algorithms-gui-impl.jar:Lib/Images.jar

								:Lib/jaxp.jar:Lib/parser.jar:Lib/jconn2.jar

								:Lib/jai_core.jar:Lib/jai_codec.jar:Lib/xerces.jar

								:Lib/base64.jar:Lib/HTTPClient.jar

								:Lib/JSciCore.jar:Lib/jama.jar:."

								org.tigr.microarray.mev.TMEV

Q. How do I get TMEV to run on MacOSX?

A. Try double-clicking on the file called TMEV_MacOSX_2_2. If the program does not launch, you may have an older version of the program with a broken application file. You can download a new one from the website.

Q. When I try to launch TMEV in Windows, a black window opens and closes again very quickly.

A. There are two possibilities. The first one is that you do not have Java installed on your computer. You can download it from the Sun website or find the file "j2re-1_3_1_08-windows-i586.exe" in the "Java" directory on your TM4 CD. Run the installer and follow the prompts. For a simple installation, accept the defaults that are presented.

If Java v1.4.2 is already installed, you probably have an older version of the TMEV.bat file. Changes in Java made for version 1.4.2 made the older versions of the TMEV.bat file unuseable. Simply download a new version from the TM4 web site.

Q. When loading my data into a Multiple Array Viewer, I get the error no more tokens. What does this mean?

A. This error usually occurs when something is wrong with the input file format. Be sure the file is saved as tab-delimited text. Each item on a line should be separated from the others by only one tab character - be especially careful that there are no spaces next to the tabs and extra tab characters at the ends of the lines. Open your input data file in a program like Excel and check that none of the cells are empty. Fill empty cells with values like "0" or N/A, depending on the type of data in them.

Q. When I save a cluster I can't re-open it in the same Multiple Array Viewer window. I get an error like:
java.lang.ArrayIndexOutOfBoundsException: 1>=1 at java.util.Vector.elementAt(Unknown Source) at org.tigr.microarray.mev.SlideData.setIntensities(SlideData.java:129)

A. The preferences file you are using for your original data will not always work with the cluster data you have saved. You need to create a new preferences file which matches the format of the saved cluster file. See the MeV manual for a description of the preferences file format and instructions on how to make a custom preferences file.

Q. When I start TMEV, I get the following error message:
Exception in thread "main" java.lang.NoClassDefFoundError: org/tigr/microarray/new/cluster/algorithm /AlgorithmFactory

A. TMEV cannot find the file algorithms.jar. This file should be located in the TMEV/lib directory. If this file is missing, just download TMEV again and reinstall.

Q. When I try to run the PCA module, I get an error like this:
java.lang.NoClassDefFoundError: javax/media/j3d/Group at org.tigr.microarray.mev.cluster.gui.impl.pca .PCA3DViewer.createContent

A. The problem is likely with the version of the JRE Java3D that you are using. Try reinstalling or updating Java3D.

Q. Why are the Eigenvalues and Eigenvectors from PCAG (PCA from genes) and PCAE (PCA from experiments) the same?

A. To compute the principal components, the m Eigenvalues and their corresponding Eigenvectors are calculated from the (m x m) distance matrix using Singular Value Decomposition (SVD). m = number of experiments. n = number o genes. Genesis uses this method for both cases (genes AND experiments)! See also answer to question (3).

Q. PCAE (PCA from experiments): If I load a data set with 30 genes and 5 conditions, I expect to see 30 components with 30 dimensions each and not only 5 components. Furthermore, the Eigenvalues should be different from those that I get with PCAG (PCA form genes).

A. This is correct, and the straightforward implementation did exactly calculate the SVD of the (n x n) distance matrix. In this case we get the expected n components, where n is the number of genes. However, the disadvantage of this method is, that it is very computational intensive, since n is usually quite large.

And here is the trick. It is due to a mathematical tick possible to calculate the result using the small (m x m, m = number of experiments) distance matrix and than calculate with the SVD of this matrix back to the required solution (PCAE).

The results of this shortcut are the same as using the straightforward method, however since we are calculating the SVD also form the small matrix, you have of course the same Eigenvalues as calculating PCA from genes.

The gain is remarkable. Lets say we have 10000 genes and 100 experiments. In this case you have to calculate the SVD of a 100x100 distance matrix (5000 elements) instead of a 10000x10000 matrix (50.000.000 elements), or in other words: 1 sec instead of a couple of hours!

Q. MeV will not print images or save images to file or specifically has problems printing a PCA image.

A. The problem existed in an early 2.2 release. The defective version was replaced and the 2.2 release currently available (as of 8/21/2003) has the repair.

Q. MeV works but TTest and ANOVA do not display results.

A. An early release of version 2.2 contained a faulty TMEV.bat file. To remedy either download a new version or edit TMEV.bat to include Lib/JSciCore.jar in the line where the classpath is set.

Q. The FOM input dialog has input fields that are compressed and unusable. (Mac Users only)

A. User interface rendering differences between Mac and other platforms caused this dialog to be compressed. This has been repaired and became available for download on 8/13/2003, 3pm EST.

Q. When loading large Stanford format files several possible behaviors make it difficult to work with the file loader interface. (Compressed columns in the expression table, lack of horizontal scrolling, or slow response.)

A. The updated 2.2 release on 8/13/2003, 3pm EST, fixed these problems.

Q. HCL Support Trees build on experiments do not resize according to the specified dimensions when altering the tree properties.

A. The updated 2.2 release on 8/21/2003 included a repair for this problem.

Q. When I load my affy data, most of the data in the main display is red. I have tried to adjust the ratio scale but it does not seem to help. Why is that?

A. The reason it is red is that affy data is positive and only uses the right side (black --> red side) of the gradient. You will need to rescale your data because of the magnitude of the values. What is important to note is that it takes a log base 2 of the intensity so when you adjust the color range in the display menu use about +-10 or 15 and your data should show as a nice gradient in the black to red range.

Q. Whenever I try to run the PCA, I am unable to view the results. I do have Java 3d installed in the right directory.

A. Make sure you have installed Java3D open GL version instead of Java3D DirectX version.

Q. How do I fix this Java.lang.outofmemory error?

A. Sometimes huge data sets can cause out of memory errors. For some algorithms (notably HCL), we get out of memory errors if the number of genes is larger than about 10,000.

If you are using a PC or a Linux machine, you can edit the TMEV.bat file (the file that you double-click on to start MeV) in a text editor and change the memory allocation. To this, find the text "java -Xmx512m" in the file, and replace 512 with 768 or 1024.

If you are using mac, click on Mev_MacOSX_2_2. Select "show package contents". Open 'contents' folder. Click on Info.plist. Open it in a text editor. You will see the following key and related string in the file:
<key> VMOptions </key>
<string> -Xmx256m </string>

Just change the 512 to 768 or 1024 and save the file.

Whatever platform you are using, be sure to allocate less memory to Java than the total amount of memory on your system. If you try to give Java 1024Mb of memory on a system that has only 512, MeV will not start.

Q. What are the hardware/software spec required to run MeV?

A. Supported Platforms: PC, Unix, Mac.
Operating Systems: Windows 2000, Windows XP, Linux, Solaris, Mac-OS10.x.
Processor Speed: >500MB suggested for best performance speed.
Memory: 256MB minimum, 512MB or more improves performance.

Q. When loading .mev and annotation files, the progress bar stalls. The black console window shows the error java.lang.NegativeArraySizeException.

A. Try checking the "Remove Annotation Quotes" box in the mev file loader. This option will remove any quotation marks that may have been added to your mev file by a certain popular spreadsheet program. These quotation marks can cause problems in MeV. If your version of MeV doesn't have this option, either upgrade to version 3.0 or higher, or edit your annotation file so that it contains no quotation marks in the Date field at the top. You will not be able to see these quotes if you open the file in the aforementioned spreadsheet program - use a text editor like Wordpad or Simpletext instead.

AMP Questions

Q. When will AMP be released?

A. AMP was first released on December 30th, 2004.