lumi-package |
A package for preprocessing Illumina microarray data |
addNuId2lumi |
Add the nuID information to the LumiBatch object |
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 |
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 |
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 in each sample |
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 |
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 estimation of the LumiBatch object |
lumiR |
Read in Illumina expression data |
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 |
plotSampleRelation |
visualize the sample relations |
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 |
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 |