BeadArray Specific Methods for Illumina Microarrays


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Documentation for package ‘lumi’ version 1.8.3

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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
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<-,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<-,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
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