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

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.

AuthorVojtech Kulvait
Date of publicationNone
MaintainerVojtech Kulvait <kulvait@gmail.com>
LicenseGPL-3
Version1.8.0
https://bitbucket.org/kulvait/blima

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

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