spikeLI: Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool

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).

Author
Delphine Baillon, Paul Leclercq <paulleclercq@hotmail.com>, Sarah Ternisien, Thomas Heim, Enrico Carlon <enrico.carlon@fys.kuleuven.be>
Date of publication
None
Maintainer
Enrico Carlon <enrico.carlon@fys.kuleuven.be>
License
GPL-2
Version
2.34.0

View on Bioconductor

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...

Files in this package

spikeLI/DESCRIPTION
spikeLI/NAMESPACE
spikeLI/R
spikeLI/R/IvsDG.R
spikeLI/R/Ivsc.R
spikeLI/R/collapse.R
spikeLI/R/zzz.R
spikeLI/build
spikeLI/build/vignette.rds
spikeLI/data
spikeLI/data/SPIKE_IN.rda
spikeLI/data/SPIKE_IN95.rda
spikeLI/data/SPIKE_INA.rda
spikeLI/data/SPIKE_INB.rda
spikeLI/data/SPIKE_INH.rda
spikeLI/data/conc133.rda
spikeLI/data/conc95.rda
spikeLI/data/hgu.rda
spikeLI/demo
spikeLI/demo/00Index
spikeLI/demo/spikeLI.R
spikeLI/inst
spikeLI/inst/doc
spikeLI/inst/doc/spikeLI.Rnw
spikeLI/inst/doc/spikeLI.pdf
spikeLI/man
spikeLI/man/IvsDG.Rd
spikeLI/man/Ivsc.Rd
spikeLI/man/SPIKE_IN.Rd
spikeLI/man/SPIKE_IN95.Rd
spikeLI/man/SPIKE_INA.Rd
spikeLI/man/SPIKE_INB.Rd
spikeLI/man/SPIKE_INH.Rd
spikeLI/man/collapse.Rd
spikeLI/man/conc133.Rd
spikeLI/man/conc95.Rd
spikeLI/man/hgu.Rd
spikeLI/man/spikeLI.package.Rd
spikeLI/vignettes
spikeLI/vignettes/IvsDG_TagE.pdf
spikeLI/vignettes/Ivsc.pdf
spikeLI/vignettes/collapse_A14.pdf
spikeLI/vignettes/langmuir2.pdf
spikeLI/vignettes/spikeLI.Rnw