blima: Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level
Version 1.10.0

Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.

AuthorVojtěch Kulvait
Bioconductor views Microarray Normalization Preprocessing
Date of publicationNone
MaintainerVojtěch Kulvait <kulvait@gmail.com>
LicenseGPL-3
Version1.10.0
URL https://bitbucket.org/kulvait/blima
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("blima")

Getting started

Package overview

Popular man pages

backgroundChannelSubtractSingleArray: Background channel subtraction
channelExistsIntegrityWithLogicalVectorList: Internal function
doProbeTTests: T-test for probe level data.
interpolateSortedVector: Interpolate sorted vector
performXieCorrection: INTERNAL FUNCTION Xie background correct.
selectedChannelTransformSingleArray: Channel transformation
varianceBeadStabiliseSingleArray: Bead level VST.
See all...

All man pages Function index File listing

Man pages

aggregateAndPreprocess: Aggregate data
bacgroundCorrect: Data background correction.
bacgroundCorrectSingleArray: Data background correction.
backgroundChannelSubtract: Background channel subtraction
backgroundChannelSubtractSingleArray: Background channel subtraction
blima-package: Package for the preprocessing and analysis of the Illumina...
channelExistsIntegrityWithLogicalVectorList: Internal function
checkIntegrity: Internal function
checkIntegrityLogical: Internal function
checkIntegrityOfListOfBeadLevelDataObjects: Internal function
checkIntegrityOfSingleBeadLevelDataObject: Internal function
chipArrayStatistics: Statistics of beadLevelData
createSummarizedMatrix: Summarized value matrix.
doAction: Internal function
doProbeTTests: T-test for probe level data.
doTTests: T-test for bead (detector) level data.
filterBg: Bg correct vector
getNextVector: Support probe and beadl level testing.
initMeanDistribution: initMeanDistribution
insertColumn: Internal function to support chipArrayStatistics
interpolateSortedVector: Interpolate sorted vector
interpolateSortedVectorRcpp_: interpolateSortedVectorRcpp
log2TransformPositive: Log2 transform of numbers >1.
meanDistribution: Produce sorted double vector with mean distribution.
nonParametricEstimator: INTERNAL FUNCTION Xie background correct.
nonPositiveCorrect: Correct non positive
nonPositiveCorrectSingleArray: Correct non positive
numberOfDistributionElements: Internal
performXieCorrection: INTERNAL FUNCTION Xie background correct.
plotBackgroundImageAfterCorrection: Plot background image after correction
plotBackgroundImageBeforeCorrection: Plot background image before correction
quantileNormalize: Bead level quantile normalization.
readToVector: Support doTTests function.
selectedChannelTransform: Channel transformation
selectedChannelTransformSingleArray: Channel transformation
singleArrayNormalize: Bead level quantile normalization.
singleChannelExistsIntegrityWithLogicalVector: Internal function
singleCheckIntegrityLogicalVector: Internal function
singleNumberOfDistributionElements: Internal
updateMeanDistribution: updateMeanDistribution
varianceBeadStabilise: Bead level VST.
varianceBeadStabiliseSingleArray: Bead level VST.
vstFromLumi: Function from LGPL lumi package 2.16.0
writeBackgroundImages: Write Background Images
xieBacgroundCorrect: Xie background correct.
xieBacgroundCorrectSingleArray: INTERNAL FUNCTION Xie background correct.

Functions

aggregateAndPreprocess Man page Source code
bacgroundCorrect Man page
bacgroundCorrectSingleArray Man page Source code
backgroundChannelSubtract Man page
backgroundChannelSubtractSingleArray Man page Source code
blima Man page
blima-package Man page
channelExistsIntegrityWithLogicalVectorList Man page Source code
checkIntegrity Man page Source code
checkIntegrityLogical Man page Source code
checkIntegrityOfListOfBeadLevelDataObjects Man page Source code
checkIntegrityOfSingleBeadLevelDataObject Man page Source code
chipArrayStatistics Man page
createSummarizedMatrix Man page
doAction Man page Source code
doProbeTTests Man page
doTTests Man page
filterBg Man page Source code
getNextVector Man page Source code
initMeanDistribution Man page Source code
insertColumn Man page Source code
interpolateSortedVector Man page Source code
interpolateSortedVectorRcpp_ Man page Source code
log2TransformPositive Man page
meanDistribution Man page Source code
nonParametricEstimator Man page Source code
nonPositiveCorrect Man page
nonPositiveCorrectSingleArray Man page Source code
numberOfDistributionElements Man page Source code
performXieCorrection Man page Source code
plotBackgroundImageAfterCorrection Man page
plotBackgroundImageBeforeCorrection Man page
quantileNormalize Man page
readToVector Man page Source code
selectedChannelTransform Man page
selectedChannelTransformSingleArray Man page Source code
singleArrayNormalize Man page Source code
singleChannelExistsIntegrityWithLogicalVector Man page Source code
singleCheckIntegrityLogicalVector Man page Source code
singleNumberOfDistributionElements Man page Source code
updateMeanDistribution Man page Source code
varianceBeadStabilise Man page
varianceBeadStabiliseSingleArray Man page Source code
vstFromLumi Man page Source code
writeBackgroundImages Man page
xieBacgroundCorrect Man page
xieBacgroundCorrectSingleArray Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/RcppExports.R
R/analyzeBeadLevel.R
R/analyzeProbeLevel.R
R/bgCorrect.R
R/quantileNormalize.R
R/reporting.R
R/standardbgCorrect.R
R/statisticsAndVisualisation.R
R/utils.R
R/vst.R
build
build/partial.rdb
build/vignette.rds
inst
inst/blima-package.Rd
inst/doc
inst/doc/blima.R
inst/doc/blima.pdf
inst/doc/blima.rnw
man
man/aggregateAndPreprocess.Rd
man/bacgroundCorrect.Rd
man/bacgroundCorrectSingleArray.Rd
man/backgroundChannelSubtract.Rd
man/backgroundChannelSubtractSingleArray.Rd
man/blima-package.Rd
man/channelExistsIntegrityWithLogicalVectorList.Rd
man/checkIntegrity.Rd
man/checkIntegrityLogical.Rd
man/checkIntegrityOfListOfBeadLevelDataObjects.Rd
man/checkIntegrityOfSingleBeadLevelDataObject.Rd
man/chipArrayStatistics.Rd
man/createSummarizedMatrix.Rd
man/doAction.Rd
man/doProbeTTests.Rd
man/doTTests.Rd
man/filterBg.Rd
man/getNextVector.Rd
man/initMeanDistribution.Rd
man/insertColumn.Rd
man/interpolateSortedVector.Rd
man/interpolateSortedVectorRcpp_.Rd
man/log2TransformPositive.Rd
man/meanDistribution.Rd
man/nonParametricEstimator.Rd
man/nonPositiveCorrect.Rd
man/nonPositiveCorrectSingleArray.Rd
man/numberOfDistributionElements.Rd
man/performXieCorrection.Rd
man/plotBackgroundImageAfterCorrection.Rd
man/plotBackgroundImageBeforeCorrection.Rd
man/quantileNormalize.Rd
man/readToVector.Rd
man/selectedChannelTransform.Rd
man/selectedChannelTransformSingleArray.Rd
man/singleArrayNormalize.Rd
man/singleChannelExistsIntegrityWithLogicalVector.Rd
man/singleCheckIntegrityLogicalVector.Rd
man/singleNumberOfDistributionElements.Rd
man/updateMeanDistribution.Rd
man/varianceBeadStabilise.Rd
man/varianceBeadStabiliseSingleArray.Rd
man/vstFromLumi.Rd
man/writeBackgroundImages.Rd
man/xieBacgroundCorrect.Rd
man/xieBacgroundCorrectSingleArray.Rd
src
src/RcppExports.cpp
src/interpolateSortedVector.cpp
vignettes
vignettes/bibliography.bib
vignettes/blima.rnw
vignettes/content
vignettes/content/01introduction01.tex
vignettes/content/01introduction02.tex
vignettes/content/01introduction03.tex
vignettes/content/02backgroundCorrection01.tex
vignettes/content/02backgroundCorrection02.tex
vignettes/content/02backgroundCorrection03.tex
vignettes/content/03varianceStabilizing01.tex
vignettes/content/03varianceStabilizing02.tex
vignettes/content/04quantileNormalize.tex
vignettes/content/05annotation01.tex
vignettes/content/05annotation02.tex
vignettes/content/06dataTesting01.tex
vignettes/content/06dataTesting02.tex
vignettes/content/06dataTesting03.tex
vignettes/content/07summarization.tex
blima documentation built on May 20, 2017, 9:52 p.m.

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