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Bioinformatics Advance Access originally published online on October 27, 2004
Bioinformatics 2005 21(5):687-688; doi:10.1093/bioinformatics/bti078
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

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

Henrik Bjørn Nielsen *, Laurent Gautier and Steen Knudsen

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

*To whom correspondence should be addressed.

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{at}cbs.dtu.dk


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