An expression matrix visualization is integrated in many of EXPANDER’s displays. This visualization is similar to the red-green matrix representation of Eisen et al (1998). All it does is to render the gene-expression data on the screen in color, where green indicates under expression, and red indicates over expression. Color rendering can be configured by the user in one of the following manners: (a) by setting the range (top and bottom values) of rendered values (default values are set according to the data scale, e.g. 40-1000 for non-standardized absolute intensities data) or (b) by setting the percent of values, which are to be disregarded as extreme values from each edge (by default set to 5%). The manner of color scale configuration (i.e. (a) vs. (b)) can be set via the ‘Data Matrix View’ tab in the ‘Display Settings’ dialog box, available from Options >> Settings. The red/green coloring scheme can be changed to blue/yellow (using Options >> Settings >> Display >> ‘Data Matrix View’ tab).
A color scale appears next to the matrix (upper right side). The displayed tool tip shows the probe ID and condition title corresponding to the row and column on which the cursor is placed, and the expression value in that position. The matrix toolbar contains zoom in, zoom out, reset scale (to reset zoom factor), shorten condition title and Elongate condition title tools.
Upon selecting Visualizations >> Clustered Expression Matrix, a clustered expression matrix visualization tab is added to the main window. The probes are ordered in their original order. If a clustering solution has been previously created, its’ name appears next to a radio button in the top right panel. Upon pressing this button, the order of the probes in the display changes and probe IDs are colored according to the clusters. The color index at the bottom right panel, maps each color to the index of the corresponding cluster.