Quality control and low-level analysis of BeadArrays


[Package List] [Top]

Documentation for package `beadarray' version 1.4.0

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

arrayNames Gets the array names from a BeadLevelList Object
arrayNames,BeadLevelList-method Class "BeadLevelList"
averagePixels Read BeadArray information into R
backgroundCorrect Background Correct a BeadLevelList object
backgroundCorrect,BeadLevelList,character,double,logical-method Class "BeadLevelList"
backgroundCorrect,BeadLevelList-method Background Correct a BeadLevelList object
backgroundCorrect,BeadLevelList-methods Background Correct a BeadLevelList object
backgroundNormalise Background Normalisation for Bead Summary Data objects
backgroundNormalise, ExpressionSetIllumina,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
backgroundNormalise, ExpressionSetIllumina-method Background Normalisation for Bead Summary Data objects
backgroundNormalise, ExpressionSetIllumina-methods Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
BeadChipSummary Interactive bead level plotting
BeadLevelList Class "BeadLevelList"
BeadLevelList-class Class "BeadLevelList"
BeadLevelNormalise Bead Level Normalisation
BLData BeadLevelList for the example experiment
boxplotBeads Box plot of bead intensities
BSData ExpressionSetIllumina object for the example experiment
calculateBackground Read BeadArray information into R
calculateForegroundIntensities Read BeadArray information into R
class:ExpressionSetIllumina Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
combine,ExpressionSetIllumina,ANY-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
combine,ExpressionSetIllumina,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
combineBeadLevelLists Combines data a BeadLevelList Object
combineBeadLevelLists,BeadLevelList-method Class "BeadLevelList"
copyBeadLevelList Copies a BeadLevelList Object
copyBeadLevelList,BeadLevelList-method Class "BeadLevelList"
createBeadSummaryData Produce bead averages
createBeadSummaryData, BeadLevelList-method Find Outliers
createBeadSummaryData,BeadLevelList-method Produce bead averages
Detection Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
Detection,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
DiffScore Illumina's DE statistic
dim,BeadLevelList-method Class "BeadLevelList"
displayTIFFImage Display part of a TIFF Image
ExpressionSetIllumina-class Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
exprs,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
exprs<-,ExpressionSetIllumina,ANY-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
exprs<-,ExpressionSetIllumina,matrix-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
findAllOutliers Find outliers on array
findAllOutliers, BeadLevelList-method Find Outliers
findAllOutliers-methods Find outliers on array
findBeadStatus Find Outliers
FindIlluminaSpotl Display part of a TIFF Image
getArrayData Gets the raw intensity data from a BeadLevelList object
getArrayData,BeadLevelList-method Class "BeadLevelList"
getProbeIndices Find Outliers
getProbeIndicesC Find Outliers
getProbeIntensities Find Outliers
getProbeIntensities,BeadLevelList-method Find Outliers
IdentifyBeads Display part of a TIFF Image
IdentifyIntensity Display part of a TIFF Image
imageplot imageplot for BeadArrays object
initialize,BeadLevelList-method Class "BeadLevelList"
initialize,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
LargeDataObject-class Large Data Object - class
medianNormalise Median Normalisation for BeadLevelList objects
NoBeads Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
NoBeads,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
numBeads Gets the number of beads from a BeadLevelList object
numBeads,BeadLevelList-method Class "BeadLevelList"
pData,BeadLevelList-method Class "BeadLevelList"
phenoData,BeadLevelList-method Class "BeadLevelList"
plotBeadDensities plot density of bead intensities
plotBeadIntensities Plot bead intensities
plotBeadLocations Show bead locations
plotMA Show MA plots
plotMAXY Scatter plots and MA-plots for all specified arrays
plotOnSAM Show variation between all 96 arrays
plotRG Plot bead level data: R vs G intensities
plotXY XY plots for two samples
QC Illumina quality control data
qcBeadLevel Generate simple diagnostic plots for Illumina bead level data
QCInfo Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
QCInfo,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
rankInvariantNormalise Rank Invariant Normalisation for Bead Summary data
read.pgmfile Read BeadArray information into R
readBeadLevelData Read BeadArray information into R
readBeadSummaryData Read BeadStudio gene expression output
readBeadSummaryTargets Create targets object
readBeadTargets Create targets object
readIllumina Read BeadArray information into R
readQC Read Illumina quality control information
SAMSummary Interactive bead level plotting
se.exprs,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
se.exprs<-,ExpressionSetIllumina,matrix-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
sharpen Read BeadArray information into R
show,BeadLevelList-method Class "BeadLevelList"
show,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
show,LargeDataObject-method Large Data Object - class
showTIFF Display part of a TIFF Image
[,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
[[,BeadLevelList,ANY,missing-method Class "BeadLevelList"