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.

Author
Hui Zhao, Kristof Engelen, Bart De Moor and Kathleen Marchal
Date of publication
None
Maintainer
Hui Zhao <hui.zhao@biw.kuleuven.be>
License
LGPL
Version
1.40.0

View on Bioconductor

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

Files in this package

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