CyberT is an internet-based program designed to accept data in the large data spreadsheet format that is generated as output by software typically used to analyze array experiment images. Figure D.1 shows a screen-shot of the CyberT window for analyzing control versus experimental data of the type considered in this book.

Each data element may correspond to a single measurement on the array (typical of membrane- or glass-slide-based arrays) or the result of a set of measurements (typical of Affymetrix GeneChips™). This data file is uploaded to CyberT using the “Browse” button in the CyberT browser window. Another window displays a version designed for the analysis of two-dye ratio data that is generated with glass slide arrays probed with Cy3/Cy5-labeled cDNA. Both of these CyberT applications are available for use at the UCI genomics web site (www.genomics.uci.edu). Detailed instructions for using CyberT can be accessed from this web page.

An example of the first few rows of a data file for CyberT is shown in Figure 7.4. The data file can be uploaded either as a whitespace, tab, or comma delimited text file.

After uploading the data file, the user enters experiment comments and defines the columns on which analyses will be performed. In the example shown in Figure D.2, there is only one label column containing gene names; however, any number of label columns containing other gene labels (descriptions) can be designated.