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| lumi-package | A package for preprocessing Illumina microarray data |
| 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 |
| beadNum | Class LumiBatch: contain and describe Illumina microarray data |
| beadNum,LumiBatch-method | Class LumiBatch: contain and describe Illumina microarray data |
| beadNum<-,LumiBatch,matrix-method | Class LumiBatch: contain and describe Illumina microarray data |
| bgAdjust | Background adjustment for Illumina data |
| boxplot,ExpressionSet-method | boxplot of a ExpressionSet object |
| boxplot-methods | boxplot of a ExpressionSet object |
| boxplot.ExpressionSet | boxplot of a ExpressionSet object |
| class:LumiBatch | Class LumiBatch: contain and describe Illumina microarray data |
| combine,LumiBatch,LumiBatch-method | Class LumiBatch: contain and describe Illumina microarray data |
| density,ExpressionSet-method | Density plot of a ExpressionSet object |
| density-methods | Density plot of a ExpressionSet object |
| density.ExpressionSet | Density plot of a ExpressionSet object |
| detection | Class LumiBatch: contain and describe Illumina microarray data |
| detection,LumiBatch-method | Class LumiBatch: contain and describe Illumina microarray data |
| detection<-,LumiBatch,matrix-method | Class LumiBatch: contain and describe Illumina microarray data |
| detectionCall | Estimate the detectable probe ratio |
| detectOutlier | Detect the outlier sample (or gene) |
| estimateLumiCV | Estimate the coefficient of variance matrix of LumiBatch object |
| example.lumi | Example LumiBatch object includes example data |
| getControlData | Get control probe information |
| getControlProbe | Get the control probe Ids |
| getControlType | Get the types of the control probes |
| getHistory | Class LumiBatch: contain and describe Illumina microarray data |
| getHistory,LumiBatch-method | Class LumiBatch: contain and describe Illumina microarray data |
| hist,ExpressionSet-method | Density plot of a ExpressionSet object |
| hist-methods | Density plot of a ExpressionSet object |
| hist.ExpressionSet | Density plot of a ExpressionSet object |
| id2seq | Transfer a nuID as a nucleotide sequence |
| initialize,LumiBatch-method | Class LumiBatch: contain and describe Illumina microarray data |
| inverseVST | Inverse VST transform |
| is.nuID | nuID self-identification |
| lumi | A package for preprocessing Illumina microarray data |
| lumiB | Background correction of Illumina data |
| LumiBatch | Class LumiBatch: contain and describe Illumina microarray data |
| LumiBatch-class | Class LumiBatch: contain and describe Illumina microarray 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 |
| MAplot,ExpressionSet-method | MAplot of a ExpressionSet object |
| MAplot-methods | MAplot of a ExpressionSet object |
| MAplot.ExpressionSet | MAplot of a ExpressionSet object |
| monoSmu | Monotonic smooth method |
| monoSpline | Fitting a curve with monotonic spline |
| nuID2probeID | Mapping nuID into Illumina ProbeID |
| nuID2targetID | Mapping nuID into Illumina TargetID |
| pairs,ExpressionSet-method | Pair plot of an ExpressionSet object |
| pairs-methods | Pair plot of an ExpressionSet object |
| pairs.ExpressionSet | Pair plot of an ExpressionSet object |
| plot,LumiBatch,missing-method | Plot of a LumiBatch object |
| plot,LumiBatch-method | Plot of a LumiBatch object |
| plot-methods | Plot of a LumiBatch object |
| plot.LumiBatch | 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 |
| rsn | Robust Spline Normalization between chips |
| se.exprs,LumiBatch-method | Class LumiBatch: contain and describe Illumina microarray data |
| se.exprs<-,LumiBatch,matrix-method | Class LumiBatch: contain and describe Illumina microarray data |
| seq2id | Transfer a nucleotide sequence as a nuID |
| show,LumiBatch-method | Class LumiBatch: contain and describe Illumina microarray data |
| ssn | Simple Scaling Normalization |
| summary,LumiBatch-method | Class LumiBatch: contain and describe Illumina microarray data |
| targetID2nuID | Mapping Illumina TargetID into nuID |
| vst | Variance Stabilizing Transformation |
| [,LumiBatch-method | Class LumiBatch: contain and describe Illumina microarray data |