IlluminaID2nuID         Matching Illumina IDs to nuID based on Illumina
                        ID mapping library
LumiBatch-class         Class LumiBatch: contain and describe Illumina
                        microarray data
MAplot-methods          MAplot of a ExpressionSet object
addControlData2lumi     Add the control probe data into the controlData
                        slot of LumiBatch object
addNuID2lumi            Add the nuID information to the LumiBatch
                        object
affyExpresso            Preprocess Affymetrix data by integrating VST
                        with expresso method
affyVstRma              Preprocess Affymetrix data by integrating VST
                        with RMA method
bgAdjust                Background adjustment for Illumina data
boxplot-methods         boxplot of a ExpressionSet object
density-methods         Density plot of a ExpressionSet object
detectOutlier           Detect the outlier sample (or gene)
detectionCall           Estimate the detectable probe ratio
estimateLumiCV          Estimate the coefficient of variance matrix of
                        LumiBatch object
example.lumi            Example LumiBatch object includes example data
getChipInfo             Get Illumina Chip Information based on probe
                        identifiers
getControlData          Get control probe information
getControlProbe         Get the control probe Ids
getControlType          Get the types of the control probes
getNuIDMappingInfo      get the mapping information from nuID to RefSeq
                        ID
hist-methods            Density plot of a ExpressionSet object
id2seq                  Transfer a nuID as a nucleotide sequence
inverseVST              Inverse VST transform
is.nuID                 nuID self-identification
lumi-package            A package for preprocessing Illumina microarray
                        data
lumiB                   Background correction of Illumina data
lumiExpresso            From raw Illumina probe intensities to
                        expression values
lumiN                   Between chip normalization of a LumiBatch
                        object
lumiQ                   Quality control evaluation 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
monoSmu                 Monotonic smooth method
monoSpline              Fitting a curve with monotonic spline
nuID2EntrezID           Map nuID to Entrez ID
nuID2IlluminaID         Matching nuIDs to Illumina IDs based on
                        Illumina ID mapping library
nuID2RefSeqID           Map nuID to RefSeq ID
nuID2probeID            Mapping nuID into Illumina ProbeID
nuID2targetID           Mapping nuID into Illumina TargetID
pairs-methods           Pair plot of an ExpressionSet object
plot-methods            Plot of a LumiBatch object
plotControlData         Plot the mean expression (with standard
                        deviation bar) of different type of control
                        probes
plotHousekeepingGene    Plot the housekeeping gene expression profile
plotSampleRelation      visualize the sample relations
plotStringencyGene      plot the Stringency related control probe
                        profiles
plotVST                 plot the VST (Variance Stabilizing Transform)
                        function
probeID2nuID            Mapping Illumina ProbeID as nuID
produceGEOPlatformFile
                        Produce GEO Platform Submission File in SOFT
                        format
produceGEOSampleInfoTemplate
                        Produce the template of GEO sample information
produceGEOSubmissionFile
                        Produce GEO Sample Submission File in SOFT
                        format
rankinvariant           Rank Invariant Normalization
rsn                     Robust Spline Normalization between chips
seq2id                  Transfer a nucleotide sequence as a nuID
ssn                     Simple Scaling Normalization
targetID2nuID           Mapping Illumina TargetID (GeneID) into nuID
vst                     Variance Stabilizing Transformation
