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Bioinformatics Advance Access published online on October 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti078
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received March 9, 2004
Revised September 14, 2004
Accepted September 27, 2004

Applications note

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

Henrik Bjørn Nielsen 1*, Laurent Gautier 1, and Steen Knudsen 1

1 Center for Biological Sequence Analysis BioCentrum-DTU Technical University of Denmark, Building 208 DK-2800, Lyngby, Denmark

* To whom correspondence should be addressed.
Henrik Bjørn Nielsen, E-mail: hbjorn{at}cbs.dtu.dk


  Abstract

Summary: Gene expression index calculations from Affymetrix GeneChips have been dominated by the Affymetrix MAS (Affymetrix, inc.), dChip and RMA methods (Li and Wong, 2001; Irizarry et al., 2003). 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: www.bioconductor.org/repository/devel/package/html/affypdnn.html.


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