Tigr MultiExperiment Viewer is a freely available tool for analyzing normalized microarray data. It can be used to perform statistical analysis, clustering, classification and visualization of the data.
MeV can be downloaded at http://www.tm4.org/mev.html
To get started using MeV, download the MeV quickstart manual.
A more detailed description of all functionalities can be found at the MeV manual
Training slides provided by MeV can be found here
Data in the following formats can be loaded into MeV:
After data is loaded into MeV, it can be adjusted by using the options under the Adjust Data Adjustments such as mean centering, median centering and log transformations can be done. The data can also be filtered based on quality and variance.
Remember that the expression image may look very different after a data adjustment such as log transformation is done. You may need to change the color scale limits (under Display menu) according to the limits of your adjusted data to see an accurate expression image.
The following statistical tests can be performed on the data using MeV: