# Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level

## Documentation for package ‘blima’ version 1.26.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

blima-package | Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.
aggregateAndPreprocess | Aggregate data
bacgroundCorrect | Data background correction.
bacgroundCorrectSingleArray | Data background correction.
backgroundChannelSubtract | Background channel subtraction
backgroundChannelSubtractSingleArray | Background channel subtraction
blima | Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.
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.