# BeadArray Specific Methods for Illumina Microarrays

## Documentation for package ‘lumi’ version 1.14.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## 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-method | Class LumiBatch: contain and describe Illumina microarray data
beadNum<- | Class LumiBatch: contain and describe Illumina microarray data
beadNum<--method | Class LumiBatch: contain and describe Illumina microarray data
bgAdjust | Background adjustment for Illumina data
boxplot-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-method | Class LumiBatch: contain and describe Illumina microarray data
density-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-method | Class LumiBatch: contain and describe Illumina microarray data
detection<- | Class LumiBatch: contain and describe Illumina microarray data
detection<--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-method | Class LumiBatch: contain and describe Illumina microarray data
getNuIDMappingInfo | get the mapping information from nuID to RefSeq ID
hist-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-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-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-method | Pair plot of an ExpressionSet object
pairs-methods | Pair plot of an ExpressionSet object
pairs.ExpressionSet | Pair plot of an ExpressionSet object
plot-method | Plot of a LumiBatch object
plot-methods | Plot of a LumiBatch object
plot.LumiBatch | Plot of a LumiBatch object
plotCDF | plot the cumulative distribution function of a ExpressionSet object
plotCDF-method | plot the cumulative distribution function of a ExpressionSet object
plotCDF-methods | plot the cumulative distribution function of a ExpressionSet object
plotCDF.ExpressionSet | plot the cumulative distribution function of a ExpressionSet 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<--method | Class LumiBatch: contain and describe Illumina microarray data
se.exprs | Class LumiBatch: contain and describe Illumina microarray data
se.exprs-method | Class LumiBatch: contain and describe Illumina microarray data
se.exprs<- | Class LumiBatch: contain and describe Illumina microarray data
se.exprs<--method | Class LumiBatch: contain and describe Illumina microarray data
seq2id | Transfer a nucleotide sequence as a nuID
show-method | Class LumiBatch: contain and describe Illumina microarray data
ssn | Simple Scaling Normalization
summary-method | Class LumiBatch: contain and describe Illumina microarray data
targetID2nuID | Mapping Illumina TargetID (GeneID) into nuID
vst | Variance Stabilizing Transformation
[-method | Class LumiBatch: contain and describe Illumina microarray data