Cvt2Mae Data Converter

Install Cvt2Mae on your computer

Cvt2Mae Home | Description | Download | FAQ | Appendix | Example | Revisions | Update | MAExplorer home | Help Desk

Cvt2Mae Basics

In order to use the MAExplorer data-mining tool on your cDNA or oligo tab-delimited array data, you must convert your data files into the data formats described in Appendix C and Appendix D of the MAExplorer reference manual. Although this maybe done by editing user's data files by hand into the required formats, it is a non-trivial process. Therefore we have developed a "wizard" conversion tool called Cvt2Mae to automate these conversions.

Cvt2Mae is a Java program designed to make it easier for use by researchers to use MAExplorer by helping them convert their data into the MAExplorer format. Cvt2Mae handles commercial chips such as Affymetrix, as well as other standard formats such as GenePix and Scanalyze or one-of-a-kind custom academic chips (<User-defined>). In addition, you may specify the fields of interest for the "Print file" or (GIPO or Gene-In-Plate-Order) file, and the fields containing the quantified data.

The Cvt2Mae converts specific chip information you entered into what we call an "Array Layout". This Array Layout file may be edited and saved for use in future conversions and shared with collaborators. Essentially, the Array Layout contains a set of "rules" for converting the user's data. After you have filled out the forms in Cvt2Mae, it will generate the set of converted data files and directories to be used directly with MAExplorer.

Cvt2Mae Data Conversion Steps and Tutorials

There is a detailed description on using the Cvt2Mae converter that provides the level of detail you need to use it effectively. In addition, a step by step example is provided converting Affymetrix data.

There are several slide shows describing how to use the Cvt2Mae to convert various data sets. They consist of a series of screen shots from Cvt2Mae that go through each of the steps on how to set up the parameters and convert your data. There are two for Affymetrix data, one is a downloadable PDF and other an extensive online version.


  1. Affymetrix Data with a full description (HTML)
  2. Affymetrix Data (PDF) or (PPT)
  3. GenePix Data (PDF) or (PPT)
  4. Scanalyze Data (PDF) or (PPT)
  5. <User-defined> Data (PDF) or (PPT)
  6. Incyte Data PDF

Downloading latest Cvt2Mae Version

You may freely download and install the current release of the Cvt2Mae stand-alone application. You are free to use or redistribute Cvt2Mae. You may want to review the revision history.

Download and Install Cvt2Mae.

Instructions on downloading and installing Cvt2Mae.

Update Cvt2Mae Program from

As of version 0.71.1 of Cvt2Mae, it is now possible to update the Cvt2Mae program from the program itself - rather than having to download the complete installer and then running the installer. Press the "Update Cvt2Mae" button at the lower left of the corner of Cvt2Mae when it is running. It asks if you want to update Cvt2Mae. Answer yes. This will then (1) backup the current Cvt2Mae.jar file as Cvt2Mae.jar.bkup in the directory where you had initially installed Cvt2Mae; (2) it then copies the latest Cvt2Mae.jar file from the Web site and replaces your working Cvt2Mae.jar file in your installation directory. You must restart Cvt2Mae for this to take effect. It will then use the new version of the program. This is a much less time consuming alternative than doing an entire download and reinstallation from the Web site.

Frequently Asked Questions (FAQ)

Here are some questions you might have about the Cvt2Mae data converter.


If Additional Help is Needed

Before emailing us for help, please read these Cvt2Mae Web pages to ensure that you have set the parameters correctly and have the raw data in the correct format. You might also read the Appendix C of the MAExplorer manual. MAExplorer and Cvt2Mae also create log files that might be of helpful in troubleshooting.

If you then are still having problems email the help desk. Please include:

[ MAExplorer home | Cvt2Mae home | Help desk | LECB/NCI/FCRDC ]