CALIB: Calibration model for estimating absolute expression levels from microarray data
Version 1.42.0

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.

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
Version1.42.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CALIB")

Popular man pages

adjustP2: Adjust model parameter P2
calibReadMe: View CALIB readme file
dim: Retrieve the Dimensions of an RGList\_CALIB or SpikeList...
normdata: Example of normalized data
ParameterList-class: Class "ParameterList" - List to store all the parameters
read.rg: Read RGList\_CALIB from Image Analysis Output Files
RGList_CALIB-class: Red, Green Intensity List - Class
See all...

All man pages Function index File listing

Man pages

adjustP2: Adjust model parameter P2
calibReadMe: View CALIB readme file
cbind: Combine RGList\_CALIB, SpikeList or ParameterList objects
dim: Retrieve the Dimensions of an RGList\_CALIB or SpikeList...
dimnames: Retrieve the Dimension Names of an RGList\_CALIB or SpikeList...
estimateParameter: Estimate model parameter from spikes
getColClasses: Construct colClasses vector for use within read.rg function
merge: Merge RGList\_CALIB or SpikeList objects
normalizeData: Normalization: estimation of absolute expression levels
normdata: Example of normalized data
parameter: Calibration Model parameter: ParameterList Example
ParameterList-class: Class "ParameterList" - List to store all the parameters
plotNormalizedData: plot estimated absolute levels of two conditions
plotSpikeCI: plot spike concentration vs measured intensity
plotSpikeHI: plot hybridized target vs intensity
plotSpikeRG: plot spike intensity R vs G
plotSpikeSpotError: plot spot error of spikes.
read.rg: Read RGList\_CALIB from Image Analysis Output Files
read.spike: Read SpikeList from a RGList\_CALIB and Concentration files
RG: Experiment Data: RGList\_CALIB Example
RGList_CALIB-class: Red, Green Intensity List - Class
spike: Experiment Data: SpikeList Example
SpikeList-class: Class "SpikeList" - Spike Intensity and Concentration List
subsetting: Subset of RGList\_CALIB, SpikeList or ParameterList object

Functions

ParameterList-class Man page
RG Man page
RGList_CALIB-class Man page
SpikeList-class Man page
[.ParameterList Man page
[.RGList_CALIB Man page
[.SpikeList Man page
adjustP2 Man page Source code
calibReadMe Man page Source code
cbind.ParameterList Man page Source code
cbind.RGList_CALIB Man page Source code
cbind.SpikeList Man page Source code
coerce,RGList_CALIB,exprSet2-method Man page
dim.RGList_CALIB Man page Source code
dim.SpikeList Man page Source code
dimnames.RGList_CALIB Man page Source code
dimnames.SpikeList Man page Source code
estimateParameter Man page Source code
getColClasses Man page Source code
length.RGList_CALIB Man page Source code
length.SpikeList Man page Source code
merge.RGList_CALIB Man page Source code
merge.SpikeList Man page Source code
normalizeData Man page Source code
normdata Man page
parameter Man page
plotNormalizedData Man page Source code
plotSpikeCI Man page Source code
plotSpikeHI Man page Source code
plotSpikeRG Man page Source code
plotSpikeSpotError Man page Source code
rbind.RGList_CALIB Man page Source code
rbind.SpikeList Man page Source code
read.rg Man page Source code
read.spike Man page Source code
show,ParameterList-method Man page
show,RGList_CALIB-method Man page
show,SpikeList-method Man page
spike 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
CALIB documentation built on May 20, 2017, 10:48 p.m.

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