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

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

Henrik Bjørn Nielsen·Laurent Gautier·Steen Knudsen

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Abstract

UNLABELLED: 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.

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Algorithms Computer Simulation Gene Expression Profiling Models, Genetic Models, Statistical Oligonucleotide Array Sequence Analysis Sequence Analysis, DNA Software Evaluation Study Journal Article

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Henrik Bjørn Nielsen, Laurent Gautier, Steen Knudsen. 2004-10-27. Implementation of a gene expression index calculation method based on the PDNN model.. https://doi.org/10.1093/bioinformatics%2Fbti078

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