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" |