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
addAnnotationInfo       Add probe color channel and basic annotation
                        information based on the annotation library of
                        Illumina methylation microarray
addControlData2lumi     Add the control probe data into the controlData
                        slot of LumiBatch object
addControlData2methyLumiM
                        Add methylation control data to a MethyLumiM
                        object
addNuID2lumi            Add the nuID information to the LumiBatch
                        object
adjColorBias.quantile   Color bias adjustment of Illumina Infinium
                        methylaton microarrays using smooth quantile
                        normalization
adjColorBias.ssn        Color bias adjustment of Illumina Infinium
                        methylaton microarrays using simple shift and
                        scaling normalization
asBigMatrix-methods     convert the data matrix in the assayData of a
                        ExpressionSet as BigMatrix
beta2m                  Convert methylation Beta-value to M-value
bgAdjust                Background adjustment for Illumina data
bgAdjustMethylation     Estimate and adjust the background levels of
                        Illumina Infinium methylaton microarrays
boxplot,MethyLumiM-method
                        boxplot of a MethyLumiM object
boxplot-methods         boxplot of a ExpressionSet object
boxplotColorBias        Plot the Illumina Infinium methylation color
                        bias in terms of boxplot
colorBiasSummary        A summary of colorBias information
density-methods         Density plot of a ExpressionSet object
detectOutlier           Detect the outlier sample (or gene)
detectionCall           Estimate the detectable probe ratio
estimateBeta            Estimate methylation Beta-value matrix
estimateIntensity       Estimate intensity of Illumina methylation data
estimateLumiCV          Estimate the coefficient of variance matrix of
                        LumiBatch object
estimateM               Estimate methylation M-value matrix
estimateMethylationBG   Estimate the background levels of Illumina
                        Infinium methylaton microarrays
example.lumi            Example Illumina Expression data in LumiBatch
                        class
example.lumiMethy       Example Illumina Infinium Methylation data in
                        MethyLumiM class
example.methyTitration
                        Example Illumina Infinium Methylation titration
                        data in MethyLumiM class
gammaFitEM              Estimate the methylation status by fitting a
                        Gamma mixture model using EM algorithm
getChipInfo             Get Illumina Chip Information based on probe
                        identifiers
getChrInfo              get the chromosome location information of
                        methylation probes
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
importMethyIDAT         Import Illumina methylation .idat files as an
                        MethyLumiM object
inverseVST              Inverse VST transform
is.nuID                 nuID self-identification
lumi-package            A package for preprocessing Illumina microarray
                        data
lumiB                   Background correction of Illumina Expression
                        data
lumiExpresso            From raw Illumina probe intensities to
                        expression values
lumiMethyB              Adjust background level of Illumina Infinium
                        methylation data
lumiMethyC              Color bias adjust of Illumina Infinium
                        methylation data
lumiMethyN              Normalize the Illumina Infinium methylation
                        data
lumiMethyR              Reading Illumina methylation microarray data
lumiMethyStatus         Estimate the methylation status of individual
                        methylation sites
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
m2beta                  Convert methylation M-value to Beta-value
methylationCall         Estimated methylation call
monoSmu                 Monotonic smooth method
monoSpline              Fitting a curve with monotonic spline
normalizeMethylation.quantile
                        Quantile normalization of Illumina Infinium
                        methylation data at probe level
normalizeMethylation.ssn
                        Shift and scaling normalization of Illumina
                        Infinium methylation data at probe level
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 ExpressionSet object
plotCDF                 plot the cumulative distribution function of a
                        ExpressionSet object
plotColorBias1D         Plot the color bias density plot of Illumina
                        Infinium Methylation data
plotColorBias2D         Plot the color bias of Illumina Infinium
                        Methylation data in two dimensions
plotControlData         Plot the mean expression (with standard
                        deviation bar) of different type of control
                        probes
plotDensity             plot the density distribution
plotGammaFit            plot the fitting results of 'gammaFitEM'
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
produceMethylationGEOSubmissionFile
                        Produce GEO Sample Submission File of Illumina
                        methylation microarray data in SOFT format
rankinvariant           Rank Invariant Normalization
rsn                     Robust Spline Normalization between chips
seq2id                  Transfer a nucleotide sequence as a nuID
smoothQuantileNormalization
                        Smooth quantile normalization
ssn                     Simple Scaling Normalization
targetID2nuID           Mapping Illumina TargetID (GeneID) into nuID
vst                     Variance Stabilizing Transformation
