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


BACKGROUND
The package can be downloaded from http://www.bioconductor.org/repository/devel/package/html/affypdnn.html


BACKGROUND
hbjorn@cbs.dtu.dk.
Nielsen
Henrik Bjørn
HB
Center for Biological Sequence Analysis, BioCentrum-DTU Technical University of Denmark Building 208, DK-2800 Lyngby, Denmark. hbjorn@cbs.dtu.dk
Gautier
Laurent
L
Knudsen
Steen
S
D000465:Algorithms; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software