spikeLI: Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
Version 2.36.0

SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006).

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AuthorDelphine Baillon, Paul Leclercq <paulleclercq@hotmail.com>, Sarah Ternisien, Thomas Heim, Enrico Carlon <enrico.carlon@fys.kuleuven.be>
Bioconductor views Microarray QualityControl
Date of publicationNone
MaintainerEnrico Carlon <enrico.carlon@fys.kuleuven.be>
LicenseGPL-2
Version2.36.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("spikeLI")

Man pages

collapse: Data collapse of all concentrations into a single graph
conc133: Concentration 95
conc95: Concentration 95
hgu: Selected Probe Set data
Ivsc: Plot of intensity vs. concentration for given probes
IvsDG: Plot Intensity as function of the affinity for a given probe...
SPIKE_IN: Spike-in Probe-Set Names
SPIKE_IN95: set of spike-in genes contained in the HGU95 dataset
SPIKE_INA: Artificial Spike-in probesets
SPIKE_INB: Bacteria Spike-in probeset names
SPIKE_INH: Human Spike-in probe-set names
spikeLI.package: Analysis of Affymetrix spike-in data (HGU95 and HGU133 Latin...

Functions

IvsDG Man page Source code
Ivsc Man page Source code
SPIKE_IN Man page
SPIKE_IN95 Man page
SPIKE_INA Man page
SPIKE_INB Man page
SPIKE_INH Man page
collapse Man page
conc133 Man page
conc95 Man page
hgu Man page
onAttach Source code
spikeLI Man page
spikeLI-package Man page

Files

DESCRIPTION
NAMESPACE
R
R/IvsDG.R
R/Ivsc.R
R/collapse.R
R/zzz.R
build
build/vignette.rds
data
data/SPIKE_IN.rda
data/SPIKE_IN95.rda
data/SPIKE_INA.rda
data/SPIKE_INB.rda
data/SPIKE_INH.rda
data/conc133.rda
data/conc95.rda
data/hgu.rda
demo
demo/00Index
demo/spikeLI.R
inst
inst/doc
inst/doc/spikeLI.Rnw
inst/doc/spikeLI.pdf
man
man/IvsDG.Rd
man/Ivsc.Rd
man/SPIKE_IN.Rd
man/SPIKE_IN95.Rd
man/SPIKE_INA.Rd
man/SPIKE_INB.Rd
man/SPIKE_INH.Rd
man/collapse.Rd
man/conc133.Rd
man/conc95.Rd
man/hgu.Rd
man/spikeLI.package.Rd
vignettes
vignettes/IvsDG_TagE.pdf
vignettes/Ivsc.pdf
vignettes/collapse_A14.pdf
vignettes/langmuir2.pdf
vignettes/spikeLI.Rnw
spikeLI documentation built on May 20, 2017, 9:24 p.m.