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Overview

This manual describes the GENE application. GENE stands for Gene Expression and Normalization Engine, a program designed to calculate gene expressions from Affymetrix CEL files. It implements two of the more popular methods, MAS 5.0 and RMA, in a graphical interface for easy end-user access.

GENE does not provide any microarray analysis, it merely computes the gene expression from raw Affymetrix CEL files. It does so easily and efficiently, such that many CEL files can be processed with modest resources.

In order to use GENE you will need access to the CDF file from Affymetrix, which describes the design of the chip. With the CEL files and the corresponding CDF file, GENE will generate a single tab-delimited text file containing the normalized gene expression values. This file is suitable for loading into Microsoft Excel or Bioconductor (R) for further analysis.

The GENE application is a graphical application with a simple tabbed window interface. There are three tabs: CEL Files, RMA, and MAS5.0. Each section is described individually in this manual. A Log Window, at the bottom of the application, is used for displaying important information throughout the execution of GENE.
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