# BeadArray Specific Methods for Illumina Microarrays

## Documentation for package ‘lumi’ version 1.12.4

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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
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,ExpressionSet-method | Class LumiBatch: contain and describe Illumina microarray data
beadNum<- | Class LumiBatch: contain and describe Illumina microarray data
beadNum<-,ExpressionSet-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,ExpressionSet,LumiBatch-method | Class LumiBatch: contain and describe Illumina microarray data
combine,LumiBatch,ExpressionSet-method | 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,ExpressionSet-method | Class LumiBatch: contain and describe Illumina microarray data
detection<- | Class LumiBatch: contain and describe Illumina microarray data
detection<-,ExpressionSet-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
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
getHistory | Class LumiBatch: contain and describe Illumina microarray data
getHistory,LumiBatch-method | Class LumiBatch: contain and describe Illumina microarray data
getNuIDMappingInfo | get the mapping information from nuID to RefSeq ID
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
IlluminaID2nuID | Matching Illumina IDs to nuID based on Illumina ID mapping library
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
nuID2EntrezID | Map nuID to Entrez ID
nuID2IlluminaID | Matching nuIDs to Illumina IDs based on Illumina ID mapping library
nuID2probeID | Mapping nuID into Illumina ProbeID
nuID2RefSeqID | Map nuID to RefSeq ID
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
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
sampleNames<-,LumiBatch,ANY-method | Class LumiBatch: contain and describe Illumina microarray data
se.exprs | Class LumiBatch: contain and describe Illumina microarray data
se.exprs,ExpressionSet-method | Class LumiBatch: contain and describe Illumina microarray data
se.exprs<- | Class LumiBatch: contain and describe Illumina microarray data
se.exprs<-,ExpressionSet-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 (GeneID) into nuID
vst | Variance Stabilizing Transformation
[,LumiBatch-method | Class LumiBatch: contain and describe Illumina microarray data