Implementation of a gene expression index calculation method based on the PDNN model

Abstract

Summary: Gene expression index calculations from Affymetrix GeneChips have been dominated by the Affymetrix MAS, dChip, and RMA methods. A new method to estimate the gene expression value utilizing the probe sequence information named position-dependent nearest-neighbor (PDNN) has been suggested by Zhang et al. (2003). Here we describe an open source implementation of the PDNN method for the statistical language R. Availability: The package can be downloaded from http://www.bioconductor.org/repository/devel/package/html/affypdnn.html Contact:hbjorn@cbs.dtu.dk