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 |