A B C D E F G I L M N O P Q R S V misc
addArrayMask | Array Mask |
arrayNames | Gets the strip/array names from a BeadLevelList Object |
arrayNames,BeadLevelList-method | Class "BeadLevelList" |
backgroundControlPlot | QA measures based on bead-level negative controls |
backgroundCorrect | Background correct a BeadLevelList object |
backgroundCorrect,BeadLevelList,character,double,logical-method | Class "BeadLevelList" |
backgroundCorrect,BeadLevelList-method | Background correct a BeadLevelList object |
BASH | BASH - BeadArray Subversion of Harshlight |
BASHCompact | BASH - Compact Defect Analysis |
BASHDiffuse | BASH - Diffuse Defect Analysis |
BASHExtended | BASH - Extended Defect Analysis |
beadarrayUsersGuide | View beadarray User's Guide |
BeadChipSummary | Interactive bead-level plotting |
BeadLevelList | Class "BeadLevelList" |
BeadLevelList-class | Class "BeadLevelList" |
beadResids | Calculates per strip/array bead-level residuals |
BGFilter | Background Filter |
BGFilterWeighted | Weighted Background Filter |
BLData | BeadLevelList objec from an example experiment |
boxplotBeads | Box plot of bead intensities |
BSData | ExpressionSetIllumina object for the example experiment |
calculateBeadLevelScores | Quality assessment for expression chips |
calculateDetection | Calculate detection scores |
chooseClusters | Choose Clusters |
class:ExpressionSetIllumina | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
clearArrayMask | Array Mask |
closeImage | Close Image |
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 from two BeadLevelList objects |
combineBeadLevelLists,BeadLevelList-method | Class "BeadLevelList" |
copyBeadLevelList | Copies a BeadLevelList Object |
copyBeadLevelList,BeadLevelList-method | Class "BeadLevelList" |
createBeadSummaryData | Produce bead averages |
denseRegions | Find Dense Regions of Points (as used in diffuse defect analysis). |
Detection | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
Detection,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
Detection<-,ExpressionSetIllumina,matrix-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
dim,BeadLevelList-method | Class "BeadLevelList" |
ExpressionControlData | Control annotation for Illumina expression chips |
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,matrix-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
findAllOutliers | Find outliers on a given strip/array |
findBeadStatus | Find Outliers |
generateE | Generate Error Image for BeadLevelList object |
generateNeighbours | Generate Neighbours Matrix for BeadLevelList object |
getAnnotation | Storage of annotation information for Illumina expression chips |
getArrayData | Get raw data from a BeadLevelList object |
getArrayData,BeadLevelList-method | Class "BeadLevelList" |
getControlAnno | Storage of annotation information for Illumina expression chips |
getProbeIntensities | Find Outliers |
getProbeIntensities,BeadLevelList-method | Find Outliers |
getVariance | Gets the bead-type variances from an ExpressionSetIllumina Object |
getVariance,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
gradientPlot | Quality assessment for expression chips |
imageplot | imageplot for BeadLevelList object |
initialize,BeadLevelList-method | Class "BeadLevelList" |
initialize,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
lmhPlot | Plot the bead-level hybridisation controls |
medianNormalise | Median normalise data in a matrix |
NoBeads | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
NoBeads,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
NoBeads<-,ExpressionSetIllumina,matrix-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
normaliseIllumina | Normalise Illumina expression data |
numBeads | Gets the number of beads from a BeadLevelList object |
numBeads,BeadLevelList-method | Class "BeadLevelList" |
outlierPlot | Locations of outliers on an Illumina chip |
pData,BeadLevelList-method | Class "BeadLevelList" |
phenoData,BeadLevelList-method | Class "BeadLevelList" |
plotBeadDensities | plot densities of bead intensities |
plotBeadIntensities | Plot bead intensities |
plotBeadLocations | Plot 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 |
poscontPlot | Plot bead-level housekeeping and biotin controls |
probePairsPlot | QA plot using perfect match and mismatch controls |
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. |
QCInfo<-,ExpressionSetIllumina,list-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
rankInvariantNormalise | Rank Invariant normalise data in a matrix |
readBeadSummaryData | Read BeadStudio gene expression output |
readBGX | Read Illumina .bgx file into R |
readIllumina | Read bead-level data into R |
readQC | Read Illumina control intensities |
removeArrayMask | Array Mask |
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. |
setAnnotation | Storage of annotation information for Illumina expression chips |
setWeights | Set BeadLevelList Weights |
show,BeadLevelList-method | Class "BeadLevelList" |
show,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
showArrayMask | Array Mask |
viewBeads | View Beads |
[,ExpressionSetIllumina-method | Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
[[,BeadLevelList,ANY,missing-method | Class "BeadLevelList" |