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