CELFileNormalization

This is the project page for the CELFileNormalization project. Affymetrix GeneChip data can be normalized and processed using any number of methods. We believe a tool would be useful that pre-processes the CEL file (raw data) before any of these techniques are used. The approach is simple - at the summarized image level, all chips should be adjusted to have the same general intensities.

This project consists of a java Swing application that reads in a set of CEL files, performs normalization, then writes the resulting CEL files back out. The two types of normalization that are possible include a quantile normalization (such as used in RMA, except for all possible probes on the chip) or a mean normalization (which sets the mean value of intensities on the chip as equal).

Since this program rewrites CEL files it currently works best using the old format (V3) text-based CEL files. Future work includes the read/writing of binary CEL files.

Note this project depends on jAffy for compiling. However, jar files are also available to run directly.

A zip file of all necessary jar files is available.

You can also run it via webstart.

Documentation

Background

Contacts

Andrew Hoerter, Steven Eschrich