BeadArray Specific Methods for Illumina Microarrays


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Documentation for package ‘lumi’ version 1.4.0

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lumi-package A package for preprocessing Illumina microarray data
addNuId2lumi Add the nuID information to the LumiBatch object
beadNum Class LumiBatch: contain and describe Illumina microarray data
beadNum,LumiBatch-method Class LumiBatch: contain and describe Illumina microarray data
beadNum<-,LumiBatch,matrix-method Class LumiBatch: contain and describe Illumina microarray data
bgAdjust Background adjustment for Illumina data
boxplot,ExpressionSet-method boxplot of a ExpressionSet object
boxplot-methods boxplot of a ExpressionSet object
boxplot.ExpressionSet boxplot of a ExpressionSet object
class:LumiBatch Class LumiBatch: contain and describe Illumina microarray data
combine,LumiBatch,LumiBatch-method Class LumiBatch: contain and describe Illumina microarray data
density,ExpressionSet-method Density plot of a ExpressionSet object
density-methods Density plot of a ExpressionSet object
density.ExpressionSet Density plot of a ExpressionSet object
detection Class LumiBatch: contain and describe Illumina microarray data
detection,LumiBatch-method Class LumiBatch: contain and describe Illumina microarray data
detection<-,LumiBatch,matrix-method Class LumiBatch: contain and describe Illumina microarray data
detectionCall Estimate the detectable probe ratio in each sample
detectOutlier Detect the outlier sample (or gene)
estimateLumiCV Estimate the coefficient of variance matrix of LumiBatch object
example.lumi Example lumiBatch object includes example data
getHistory Class LumiBatch: contain and describe Illumina microarray data
getHistory,LumiBatch-method Class LumiBatch: contain and describe Illumina microarray data
hist,ExpressionSet-method Density plot of a ExpressionSet object
hist-methods Density plot of a ExpressionSet object
hist.ExpressionSet Density plot of a ExpressionSet object
id2seq Transfer a nuID as a nucleotide sequence
initialize,LumiBatch-method Class LumiBatch: contain and describe Illumina microarray data
inverseVST Inverse VST transform
is.nuID nuID self-identification
lumi A package for preprocessing Illumina microarray data
lumiB Background correction of Illumina data
LumiBatch Class LumiBatch: contain and describe Illumina microarray data
LumiBatch-class Class LumiBatch: contain and describe Illumina microarray data
lumiExpresso From raw Illumina probe intensities to expression values
lumiN Between chip normalization of a LumiBatch object
lumiQ Quality control estimation of the LumiBatch object
lumiR Read in Illumina expression data
lumiR.batch Read BeadStudio output files in batch
lumiT Transfer the Illumina data to stabilize the variance
MAplot,ExpressionSet-method MAplot of a ExpressionSet object
MAplot-methods MAplot of a ExpressionSet object
MAplot.ExpressionSet MAplot of a ExpressionSet object
monoSmu Monotonic smooth method
monoSpline Fitting a curve with monotonic spline
nuID2probeID Mapping nuID into Illumina ProbeID
nuID2targetID Mapping nuID into Illumina TargetID
pairs,ExpressionSet-method Pair plot of an ExpressionSet object
pairs-methods Pair plot of an ExpressionSet object
pairs.ExpressionSet Pair plot of an ExpressionSet object
plot,LumiBatch,missing-method Plot of a LumiBatch object
plot,LumiBatch-method Plot of a LumiBatch object
plot-methods Plot of a LumiBatch object
plot.LumiBatch Plot of a LumiBatch object
plotSampleRelation visualize the sample relations
plotVST plot the VST (Variance Stabilizing Transform) function
probeID2nuID Mapping Illumina ProbeID as nuID
rsn Robust Spline Normalization between chips
se.exprs,LumiBatch-method Class LumiBatch: contain and describe Illumina microarray data
se.exprs<-,LumiBatch,matrix-method Class LumiBatch: contain and describe Illumina microarray data
seq2id Transfer a nucleotide sequence as a nuID
show,LumiBatch-method Class LumiBatch: contain and describe Illumina microarray data
summary,LumiBatch-method Class LumiBatch: contain and describe Illumina microarray data
targetID2nuID Mapping Illumina TargetID into nuID
vst Variance Stabilizing Transformation
[,LumiBatch-method Class LumiBatch: contain and describe Illumina microarray data