arrayNames |
Gets the strip/array names from a BeadLevelList Object |
arrayNames,BeadLevelList-method |
Class "BeadLevelList" |
backgroundCorrect |
Background correct a BeadLevelList object |
backgroundCorrect,BeadLevelList,character,double,logical-method |
Class "BeadLevelList" |
backgroundCorrect,BeadLevelList-method |
Background correct a BeadLevelList object |
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 |
BLData |
BeadLevelList objec from an example experiment |
boxplotBeads |
Box plot of bead intensities |
BSData |
ExpressionSetIllumina object for the example experiment |
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 from two BeadLevelList objects |
combineBeadLevelLists,BeadLevelList-method |
Class "BeadLevelList" |
copyBeadLevelList |
Copies a BeadLevelList Object |
copyBeadLevelList,BeadLevelList-method |
Class "BeadLevelList" |
createBeadSummaryData |
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. |
Detection<-,ExpressionSetIllumina,matrix-method |
Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
dim,BeadLevelList-method |
Class "BeadLevelList" |
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 |
getArrayData |
Get raw data from a BeadLevelList object |
getArrayData,BeadLevelList-method |
Class "BeadLevelList" |
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. |
imageplot |
imageplot for BeadLevelList object |
initialize,BeadLevelList-method |
Class "BeadLevelList" |
initialize,ExpressionSetIllumina-method |
Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
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" |
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 |
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 |
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. |
show,BeadLevelList-method |
Class "BeadLevelList" |
show,ExpressionSetIllumina-method |
Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
[,ExpressionSetIllumina-method |
Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays. |
[[,BeadLevelList,ANY,missing-method |
Class "BeadLevelList" |