blima: Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.

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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.

Author
Vojtech Kulvait
Date of publication
None
Maintainer
Vojtech Kulvait <kulvait@gmail.com>
License
GPL-3
Version
1.8.0
URLs

View on Bioconductor

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
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.

Files in this package

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