Entry: IlluminaID2nuID
Aliases: IlluminaID2nuID
Keywords: methods utilities
Description: Matching Illumina IDs to nuID based on Illumina ID mapping library
URL: ../../../library/lumi/html/IlluminaID2nuID.html

Entry: LumiBatch-class
Aliases: class:LumiBatch LumiBatch-class LumiBatch se.exprs se.exprs<- se.exprs,ExpressionSet-method se.exprs<-,ExpressionSet-method beadNum beadNum<- beadNum,ExpressionSet-method beadNum<-,ExpressionSet-method detection detection<- detection,ExpressionSet-method detection<-,ExpressionSet-method initialize,LumiBatch-method summary,LumiBatch-method show,LumiBatch-method combine,LumiBatch,LumiBatch-method combine,ExpressionSet,LumiBatch-method combine,LumiBatch,ExpressionSet-method [,LumiBatch-method sampleNames<-,LumiBatch,ANY-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: addControlData2lumi
Aliases: addControlData2lumi
Keywords: methods
Description: Add the control probe data into the controlData slot of LumiBatch object
URL: ../../../library/lumi/html/addControlData2lumi.html

Entry: addNuID2lumi
Aliases: addNuID2lumi addNuId2lumi
Keywords: methods
Description: Add the nuID information to the LumiBatch object
URL: ../../../library/lumi/html/addNuID2lumi.html

Entry: affyExpresso
Aliases: affyExpresso
Keywords: methods
Description: Preprocess Affymetrix data by integrating VST with expresso method
URL: ../../../library/lumi/html/affyExpresso.html

Entry: affyVstRma
Aliases: affyVstRma
Keywords: methods
Description: Preprocess Affymetrix data by integrating VST with RMA method
URL: ../../../library/lumi/html/affyVstRma.html

Entry: bgAdjust
Aliases: bgAdjust
Keywords: methods
Description: Background adjustment for Illumina data
URL: ../../../library/lumi/html/bgAdjust.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: density-methods
Aliases: density-methods density.ExpressionSet density,ExpressionSet-method
Keywords: methods hplot
Description: Density plot of a ExpressionSet object
URL: ../../../library/lumi/html/density-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
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: getChipInfo
Aliases: getChipInfo
Keywords: methods utilities
Description: Get Illumina Chip Information based on probe identifiers
URL: ../../../library/lumi/html/getChipInfo.html

Entry: getControlData
Aliases: getControlData
Keywords: methods
Description: Get control probe information
URL: ../../../library/lumi/html/getControlData.html

Entry: getControlProbe
Aliases: getControlProbe
Keywords: methods
Description: Get the control probe Ids
URL: ../../../library/lumi/html/getControlProbe.html

Entry: getControlType
Aliases: getControlType
Keywords: methods
Description: Get the types of the control probes
URL: ../../../library/lumi/html/getControlType.html

Entry: getNuIDMappingInfo
Aliases: getNuIDMappingInfo
Keywords: methods utilities
Description: get the mapping information from nuID to RefSeq ID
URL: ../../../library/lumi/html/getNuIDMappingInfo.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 evaluation 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: lumiR.batch
Aliases: lumiR.batch
Keywords: methods
Description: Read BeadStudio output files in batch
URL: ../../../library/lumi/html/lumiR.batch.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: nuID2EntrezID
Aliases: nuID2EntrezID
Keywords: methods utilities
Description: Map nuID to Entrez ID
URL: ../../../library/lumi/html/nuID2EntrezID.html

Entry: nuID2IlluminaID
Aliases: nuID2IlluminaID
Keywords: methods utilities
Description: Matching nuIDs to Illumina IDs based on Illumina ID mapping library
URL: ../../../library/lumi/html/nuID2IlluminaID.html

Entry: nuID2RefSeqID
Aliases: nuID2RefSeqID
Keywords: methods utilities
Description: Map nuID to RefSeq ID
URL: ../../../library/lumi/html/nuID2RefSeqID.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: plotControlData
Aliases: plotControlData
Keywords: methods hplot
Description: Plot the mean expression (with standard deviation bar) of different type of control probes
URL: ../../../library/lumi/html/plotControlData.html

Entry: plotHousekeepingGene
Aliases: plotHousekeepingGene
Keywords: methods hplot
Description: Plot the housekeeping gene expression profile
URL: ../../../library/lumi/html/plotHousekeepingGene.html

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

Entry: plotStringencyGene
Aliases: plotStringencyGene
Keywords: methods hplot
Description: plot the Stringency related control probe profiles
URL: ../../../library/lumi/html/plotStringencyGene.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: produceGEOPlatformFile
Aliases: produceGEOPlatformFile
Keywords: utilities
Description: Produce GEO Platform Submission File in SOFT format
URL: ../../../library/lumi/html/produceGEOPlatformFile.html

Entry: produceGEOSampleInfoTemplate
Aliases: produceGEOSampleInfoTemplate
Keywords: utilities
Description: Produce the template of GEO sample information
URL: ../../../library/lumi/html/produceGEOSampleInfoTemplate.html

Entry: produceGEOSubmissionFile
Aliases: produceGEOSubmissionFile
Keywords: utilities
Description: Produce GEO Sample Submission File in SOFT format
URL: ../../../library/lumi/html/produceGEOSubmissionFile.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: ssn
Aliases: ssn
Keywords: methods
Description: Simple Scaling Normalization
URL: ../../../library/lumi/html/ssn.html

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

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