averagePixels |
Read BeadArray information into R |
backgroundCorrect |
Background Correct a BeadLevelList object |
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 |
Class "BeadLevelList" |
BeadLevelNormalise |
Bead Level Normalisation |
BLData |
BeadLevelList for the example experiment |
BSData |
ExpressionSetIllumina object for the example experiment |
calculateBackground |
Read BeadArray information into R |
calculateForegroundIntensities |
Read BeadArray information into R |
cbind.BeadLevelList |
Combine BeadLevelList or BeadSummaryList Objects |
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. |
createBeadSummaryData |
Produce bead averages |
createBeadSummaryData, BeadLevelList-method |
Find Outliers |
createBeadSummaryData,BeadLevelList-method |
Produce bead averages |
createBeadSummaryDataSlow |
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 |
Retrieve the Dimensions of a BeadLevelList |
dimnames.BeadLevelList |
Retrieve the Dimension Names of an BeadLevelList or BeadSummaryList Object |
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,matrix-method |
Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
findAllOutliers |
Find outliers on array |
findAllOutliers, BeadLevelList-method |
Find Outliers |
findAllOutliersSlow |
Find outliers on array |
findBeadStatus |
Find Outliers |
FindIlluminaSpotl |
Display part of a TIFF Image |
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 |
imageplot, BeadLevelList-methods |
Class "BeadLevelList" |
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. |
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 |
plotQC |
Read and plot Illumina quality control information |
plotXY |
XY plots for two samples |
print.BeadLevelList |
Class "BeadLevelList" |
QC |
Illumina quality control 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 |
rbind.BeadLevelList |
Combine BeadLevelList or BeadSummaryList Objects |
read.pgmfile |
Read BeadArray information into R |
readBeadLevelData |
Read BeadArray information into R |
readBeadSummaryData |
Read bead summary data information into R |
readBeadSummaryTargets |
Create targets object |
readBeadTargets |
Create targets object |
readCols |
Read bead summary data information into R |
readQC |
Read and plot 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 |
singleQCPlot |
Read and plot Illumina quality control information |
[,ExpressionSetIllumina-method |
Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
[.BeadLevelList |
Class "BeadLevelList" |