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

Henrik Bjørn Nielsen; Laurent Gautier; Steen Knudsen

doi:10.1093/bioinformatics/bti078

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

Bioinformatics. 2005 Mar 1;21(5):687-8. doi: 10.1093/bioinformatics/bti078. Epub 2004 Oct 27.

Authors

Henrik Bjørn Nielsen¹, Laurent Gautier, Steen Knudsen

Affiliation

¹ Center for Biological Sequence Analysis, BioCentrum-DTU Technical University of Denmark Building 208, DK-2800 Lyngby, Denmark. hbjorn@cbs.dtu.dk

PMID: 15509605
DOI: 10.1093/bioinformatics/bti078

Abstract

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.

Publication types

Evaluation Study

MeSH terms

Algorithms*
Computer Simulation
Gene Expression Profiling / methods*
Models, Genetic*
Models, Statistical
Oligonucleotide Array Sequence Analysis / methods*
Sequence Analysis, DNA / methods*
Software*