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What is TMeV ?

TMeV: Tigr MultiExperiment Viewer

 

Normalized and filtered expression files can be analyzed using TIGR Multiexperiment Viewer (MeV). MeV is a versatile microarray data analysis tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery. MeV can handle several input file formats. These include the “.mev” and “.tav” files generated by TIGR Spotfinder and TIGR MIDAS, and also Affymetrix® (“.txt”) and Genepix® (“.gpr”) files. MeV generates informative and interrelated displays of expression and annotation data from single or multiple experiments. At this final stage of the TM4 pipeline, flexibility and the variety of analysis techniques are critical, as every algorithm has strengths that can be exploited when used on certain datasets and experimental designs. The concept of modularization lends itself particularly well to this system, as novel algorithms and existing codebases from the microarray community can be integrated with the Java based MeV using a well-defined module API.

 

Why has SIGENAE developed a new version of TMeV ?

The SIGENAE users store their microarray data in BASE (base.thep.lu.se). This version of TMeV enables to connect to BASE and retrieve the data very easily.

 

How do I install SIGENAE TMeV on my computer ?

First : download and install TMeV 4.1 from sourceforge.

 

 

Second : download and install two of the three files hereunder :

 

For MS-Windows and TMeV Version 4.1 :

- download sigenae_mev_*.jar,

- install sigenae_mev_*.jar in the lib directory of TMeV,

- remove mev-base.jar from the lib directory of TMeV.

 

For MS-Windows and TMeV Version 4.0 and under:

- download sigenae_mev_*.jar and sigenae-TMEV-*.bat for,

- install sigenae_mev_*.jar in the lib directory of TMeV,

- install sigenae-TMEV-*.bat in the root (where the other bat is) directory of TMeV.

 

For Linux :

- download sigenae_mev_*.jar and sigenae-TMEV-*.sh

- install sigenae_mev_*.jar in the lib directory of TMeV,

- install sigenae-TMEV-*.sh in the root (where the other bat is) directory of TMeV,

- make the sigenae-TMEV-*.sh file runnable by "chmod +x sigenae-TMEV-*.sh".

 

Third : load an example file in the Original TMeV to set the data directory.

 

Four : launch the SIGENAE TMeV.

 

How do I retrieve the data from BASE?

- File menu

- Click on BASE Connection

- Enter your BASE URL, login and password

- Click Connect

- Select the Experiement you want to work with

- Click Select

- Select the BioAssay you want to work with

- Click Load

 

NB. This can take sometime. We will add a progress bar or a line count in the next version to follow the process.

 

NB. If a file selection windows opens you should first load a TMev test dataset to set correctly the data directory path.



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