affypdnn: Probe Dependent Nearest Neighbours (PDNN) for the affy package

The package contains functions to perform the PDNN method described by Li Zhang et al.

Author
H. Bjorn Nielsen and Laurent Gautier (Many thanks to Li Zhang early communications about the existence of the PDNN program and related publications).
Date of publication
None
Maintainer
Laurent Gautier<lgautier@gmail.com>
License
LGPL
Version
1.48.0

View on Bioconductor

Man pages

chiptype.pdnn.params
Chip-type specific data
expressopdnn
Position Dependant Nearest Neighbors model for affy
find.params.pdnn
A function to find the experiment specific PDNN parameters
generateExprVal.method.pdnn
Compute PM correction and summary expression value
matplotProbesPDNN
Plot the PDNN computed probe intensities
params.dilution
Parameters for the Dilution dataset
pdnn.params.chiptype
A function to fit PDNN parameters
transform.ProbeSet
A function to transform a ProbeSet

Files in this package

affypdnn/DESCRIPTION
affypdnn/NAMESPACE
affypdnn/R
affypdnn/R/expressopdnn.R
affypdnn/R/find.params.pdnn.R
affypdnn/R/generateExprVal.method.pdnn.R
affypdnn/R/pdnn.params.chiptype.R
affypdnn/R/transform.ProbeSet.R
affypdnn/R/zzz.R
affypdnn/build
affypdnn/build/vignette.rds
affypdnn/data
affypdnn/data/datalist
affypdnn/data/hgu95av2.pdnn.params.rda
affypdnn/data/params.dilution.rda
affypdnn/inst
affypdnn/inst/CITATION
affypdnn/inst/doc
affypdnn/inst/doc/affypdnn.R
affypdnn/inst/doc/affypdnn.Rnw
affypdnn/inst/doc/affypdnn.pdf
affypdnn/inst/exampleData
affypdnn/inst/exampleData/pdnn-energy-parameter_hg-u133a.txt
affypdnn/inst/exampleData/pdnn-energy-parameter_hg-u95av2.txt
affypdnn/inst/exampleData/pdnn-energy-parameter_mg-u74av2.txt
affypdnn/man
affypdnn/man/chiptype.pdnn.params.Rd
affypdnn/man/expressopdnn.Rd
affypdnn/man/find.params.pdnn.Rd
affypdnn/man/generateExprVal.method.pdnn.Rd
affypdnn/man/matplotProbesPDNN.Rd
affypdnn/man/params.dilution.Rd
affypdnn/man/pdnn.params.chiptype.Rd
affypdnn/man/transform.ProbeSet.Rd
affypdnn/vignettes
affypdnn/vignettes/affypdnn.Rnw