Perfect Match

A tool to quantify Affymetrix microarrays. Quantifications are based on Li Zhang's "Position Dependent Nearest Neighbor" model, which makes explicit use of probe sequence information.

The manual is available online here.

Haitao Zhao, James Mitchell, and Clift Norris developed the software using Visual C++ and MFC.

Reference

Li Zhang, Michael F. Miles, Kenneth D. Aldape. "A model of molecular interactions on short oligonucleotide microarrays" Nature Biotechnology, 2003. Available online here.