Variance stabilization and calibration for microarray data


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Documentation for package `vsn' version 2.2.0

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class:vsn Class to contain result of a vsn fit
class:vsnInput Class to contain input data and parameters for vsn functions
dim,vsn-method Class to contain result of a vsn fit
dim,vsnInput-method Class to contain input data and parameters for vsn functions
exprs,vsn-method Class to contain result of a vsn fit
getIntensityMatrix Extract a matrix of microarray intensities from various kinds of objects
justvsn Normalization with vsn
justvsn,AffyBatch-method Normalization with vsn
justvsn,ExpressionSet-method Normalization with vsn
justvsn,RGList-method Normalization with vsn
justvsn-methods Normalization with vsn
kidney Intensity data for 1 cDNA slide with two adjacent tissue samples from a nephrectomy (kidney)
logLik,vsnInput-method Calculate the log likelihood and its gradient for the vsn model
logLik-methods Calculate the log likelihood and its gradient for the vsn model
lymphoma Intensity data for 8 cDNA slides with CLL and DLBL samples from the Alizadeh et al. paper in Nature 2000
meanSdPlot Plot row standard deviations versus row means
meanSdPlot,ExpressionSet-method Plot row standard deviations versus row means
meanSdPlot,exprSet-method Plot row standard deviations versus row means
meanSdPlot,matrix-method Plot row standard deviations versus row means
meanSdPlot,vsn-method Plot row standard deviations versus row means
meanSdPlot-methods Plot row standard deviations versus row means
ncol,vsn-method Class to contain result of a vsn fit
ncol,vsnInput-method Class to contain input data and parameters for vsn functions
normalize.AffyBatch.vsn Wrapper for vsn to be used as a normalization method in the package affy
nrow,vsn-method Class to contain result of a vsn fit
nrow,vsnInput-method Class to contain input data and parameters for vsn functions
plotVsnLogLik Calculate the log likelihood and its gradient for the vsn model
predict,vsn-method Apply the vsn transformation to data
sagmbAssess Simulate data and assess vsn's parameter estimation
sagmbSimulateData Simulate data and assess vsn's parameter estimation
show,vsn-method Class to contain result of a vsn fit
show,vsnInput-method Class to contain input data and parameters for vsn functions
vsn Variance stabilization and calibration for microarray data.
vsn-class Class to contain result of a vsn fit
vsn2 Fit the vsn model
vsn2,ExpressionSet-method Fit the vsn model
vsn2,matrix-method Fit the vsn model
vsn2,numeric-method Fit the vsn model
vsn2-methods Fit the vsn model
vsn2trsf Apply the vsn transformation to data
vsnh A function that transforms a matrix of microarray intensities
vsnInput Class to contain input data and parameters for vsn functions
vsnInput-class Class to contain input data and parameters for vsn functions
vsnMatrix Fit the vsn model
vsnPlotPar Plot trajectories of calibration and transformation parameters for a vsn fit
[,vsn-method Class to contain result of a vsn fit
[,vsnInput-method Class to contain input data and parameters for vsn functions