Entry: LumiBatch-class
Aliases: class:LumiBatch LumiBatch-class LumiBatch se.exprs,LumiBatch-method se.exprs<-,LumiBatch,matrix-method beadNum beadNum<- beadNum,LumiBatch-method beadNum<-,LumiBatch,matrix-method detection detection<- detection,LumiBatch-method detection<-,LumiBatch,matrix-method initialize,LumiBatch-method summary,LumiBatch-method show,LumiBatch-method combine,LumiBatch,LumiBatch-method [,LumiBatch-method getHistory,LumiBatch-method getHistory
Keywords: classes
Description: Class LumiBatch: contain and describe Illumina microarray data
URL: ../../../library/lumi/html/LumiBatch-class.html

Entry: MAplot-methods
Aliases: MAplot-methods MAplot.ExpressionSet MAplot,ExpressionSet-method
Keywords: methods hplot
Description: MAplot of a ExpressionSet object
URL: ../../../library/lumi/html/MAplot-methods.html

Entry: addNuId2lumi
Aliases: addNuId2lumi
Keywords: methods
Description: Add the nuID information to the LumiBatch object
URL: ../../../library/lumi/html/addNuId2lumi.html

Entry: boxplot-methods
Aliases: boxplot-methods boxplot.ExpressionSet boxplot,ExpressionSet-method
Keywords: methods hplot
Description: boxplot of a ExpressionSet object
URL: ../../../library/lumi/html/boxplot-methods.html

Entry: detectOutlier
Aliases: detectOutlier
Keywords: methods
Description: Detect the outlier sample (or gene)
URL: ../../../library/lumi/html/detectOutlier.html

Entry: detectionCall
Aliases: detectionCall
Keywords: methods
Description: Estimate the detectable probe ratio in each sample
URL: ../../../library/lumi/html/detectionCall.html

Entry: estimateLumiCV
Aliases: estimateLumiCV
Keywords: methods
Description: Estimate the coefficient of variance matrix of LumiBatch object
URL: ../../../library/lumi/html/estimateLumiCV.html

Entry: example.lumi
Aliases: example.lumi
Keywords: datasets
Description: Example lumiBatch object includes example data
URL: ../../../library/lumi/html/example.lumi.html

Entry: hist-methods
Aliases: hist-methods hist.ExpressionSet hist,ExpressionSet-method
Keywords: methods hplot
Description: Density plot of a ExpressionSet object
URL: ../../../library/lumi/html/hist-methods.html

Entry: id2seq
Aliases: id2seq
Keywords: methods
Description: Transfer a nuID as a nucleotide sequence
URL: ../../../library/lumi/html/id2seq.html

Entry: inverseVST
Aliases: inverseVST
Keywords: methods
Description: Inverse VST transform
URL: ../../../library/lumi/html/inverseVST.html

Entry: is.nuID
Aliases: is.nuID
Keywords: methods
Description: nuID self-identification
URL: ../../../library/lumi/html/is.nuID.html

Entry: lumi-package
Aliases: lumi-package lumi
Keywords: package
Description: A package for preprocessing Illumina microarray data
URL: ../../../library/lumi/html/lumi.package.html

Entry: lumiB
Aliases: lumiB
Keywords: methods
Description: Background correction of Illumina data
URL: ../../../library/lumi/html/lumiB.html

Entry: lumiExpresso
Aliases: lumiExpresso
Keywords: methods
Description: From raw Illumina probe intensities to expression values
URL: ../../../library/lumi/html/lumiExpresso.html

Entry: lumiN
Aliases: lumiN
Keywords: methods
Description: Between chip normalization of a LumiBatch object
URL: ../../../library/lumi/html/lumiN.html

Entry: lumiQ
Aliases: lumiQ
Keywords: methods
Description: Quality control estimation of the LumiBatch object
URL: ../../../library/lumi/html/lumiQ.html

Entry: lumiR
Aliases: lumiR
Keywords: IO
Description: Read in Illumina expression data
URL: ../../../library/lumi/html/lumiR.html

Entry: lumiT
Aliases: lumiT
Keywords: methods
Description: Transfer the Illumina data to stabilize the variance
URL: ../../../library/lumi/html/lumiT.html

Entry: monoSmu
Aliases: monoSmu
Keywords: methods
Description: Monotonic smooth method
URL: ../../../library/lumi/html/monoSmu.html

Entry: monoSpline
Aliases: monoSpline
Keywords: methods
Description: Fitting a curve with monotonic spline
URL: ../../../library/lumi/html/monoSpline.html

Entry: nuID2probeID
Aliases: nuID2probeID
Keywords: methods
Description: Mapping nuID into Illumina ProbeID
URL: ../../../library/lumi/html/nuID2probeID.html

Entry: nuID2targetID
Aliases: nuID2targetID
Keywords: methods
Description: Mapping nuID into Illumina TargetID
URL: ../../../library/lumi/html/nuID2targetID.html

Entry: pairs-methods
Aliases: pairs-methods pairs.ExpressionSet pairs,ExpressionSet-method
Keywords: methods hplot
Description: Pair plot of an ExpressionSet object
URL: ../../../library/lumi/html/pairs-methods.html

Entry: plot-methods
Aliases: plot-methods plot.LumiBatch plot,LumiBatch-method plot,LumiBatch,missing-method
Keywords: methods hplot
Description: Plot of a LumiBatch object
URL: ../../../library/lumi/html/plot-methods.html

Entry: plotSampleRelation
Aliases: plotSampleRelation
Keywords: hplot
Description: visualize the sample relations
URL: ../../../library/lumi/html/plotSampleRelation.html

Entry: plotVST
Aliases: plotVST
Keywords: hplot
Description: plot the VST (Variance Stabilizing Transform) function
URL: ../../../library/lumi/html/plotVST.html

Entry: probeID2nuID
Aliases: probeID2nuID
Keywords: methods
Description: Mapping Illumina ProbeID as nuID
URL: ../../../library/lumi/html/probeID2nuID.html

Entry: rsn
Aliases: rsn
Keywords: methods
Description: Robust Spline Normalization between chips
URL: ../../../library/lumi/html/rsn.html

Entry: seq2id
Aliases: seq2id
Keywords: methods
Description: Transfer a nucleotide sequence as a nuID
URL: ../../../library/lumi/html/seq2id.html

Entry: targetID2nuID
Aliases: targetID2nuID
Keywords: methods
Description: Mapping Illumina TargetID into nuID
URL: ../../../library/lumi/html/targetID2nuID.html

Entry: vst
Aliases: vst
Keywords: methods
Description: Variance Stabilizing Transformation
URL: ../../../library/lumi/html/vst.html
