CALIB: Calibration model for estimating absolute expression levels from microarray data

This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CALIB")
AuthorHui Zhao, Kristof Engelen, Bart De Moor and Kathleen Marchal
Bioconductor views Microarray Preprocessing TwoChannel
Date of publicationNone
MaintainerHui Zhao <hui.zhao@biw.kuleuven.be>
LicenseLGPL
Version1.40.0

View on Bioconductor

Functions

adjustP2 Man page
calibReadMe Man page
cbind.ParameterList Man page
cbind.RGList_CALIB Man page
cbind.SpikeList Man page
coerce,RGList_CALIB,exprSet2-method Man page
dimnames.RGList_CALIB Man page
dimnames.SpikeList Man page
dim.RGList_CALIB Man page
dim.SpikeList Man page
estimateParameter Man page
getColClasses Man page
length.RGList_CALIB Man page
length.SpikeList Man page
merge.RGList_CALIB Man page
merge.SpikeList Man page
normalizeData Man page
normdata Man page
parameter Man page
[.ParameterList Man page
ParameterList-class Man page
plotNormalizedData Man page
plotSpikeCI Man page
plotSpikeHI Man page
plotSpikeRG Man page
plotSpikeSpotError Man page
rbind.RGList_CALIB Man page
rbind.SpikeList Man page
read.rg Man page
read.spike Man page
RG Man page
[.RGList_CALIB Man page
RGList_CALIB-class Man page
show,ParameterList-method Man page
show,RGList_CALIB-method Man page
show,SpikeList-method Man page
spike Man page
[.SpikeList Man page
SpikeList-class Man page

Files

DESCRIPTION
NAMESPACE
R
R/all.R
build
build/vignette.rds
data
data/RG.rda
data/normdata.rda
data/parameter.rda
data/spike.rda
inst
inst/arraydata
inst/arraydata/3000177542.txt
inst/arraydata/3000177543.txt
inst/arraydata/SpotTypes.txt
inst/arraydata/annotation.txt
inst/arraydata/conc.txt
inst/arraydata/targets.txt
inst/doc
inst/doc/quickstart.R
inst/doc/quickstart.Rnw
inst/doc/quickstart.pdf
man
man/ParameterList-class.Rd man/RG.Rd man/RGList_CALIB-class.Rd man/SpikeList-class.Rd man/adjustP2.Rd man/calibReadMe.Rd man/cbind.Rd man/dim.Rd man/dimnames.Rd man/estimateParameter.Rd man/getColClasses.Rd man/merge.Rd man/normalizeData.Rd man/normdata.Rd man/parameter.Rd man/plotNormalizedData.Rd man/plotSpikeCI.Rd man/plotSpikeHI.Rd man/plotSpikeRG.Rd man/plotSpikeSpotError.Rd man/read.rg.Rd man/read.spike.Rd man/spike.Rd man/subsetting.Rd
src
src/Design.cpp
src/Design.h
src/Estimation.cpp
src/NormalizedData.cpp
src/NormalizedData.h
src/ParameterofOneArray.cpp
src/ParameterofOneArray.h
src/RawDataofOneArray.cpp
src/RawDataofOneArray.h
src/SpikeofOneArray.cpp
src/SpikeofOneArray.h
vignettes
vignettes/quickstart.Rnw
vignettes/readme.pdf

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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