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.

AuthorHui Zhao, Kristof Engelen, Bart De Moor and Kathleen Marchal
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

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

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

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All documentation is copyright its authors; we didn't write any of that.