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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("blima")
AuthorVojtech Kulvait
Bioconductor views Microarray Normalization Preprocessing
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.

Functions

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

Files

DESCRIPTION
NAMESPACE
NEWS
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/vignette.rds
inst
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/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
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

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

Please suggest features or report bugs with the GitHub issue tracker.

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