Variance stabilization and calibration for microarray data

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Documentation for package ‘vsn’ version 3.20.0

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vsn-package vsn
class:vsn Class to contain result of a vsn fit
class:vsnInput Class to contain input data and parameters for vsn functions
coef-method Class to contain result of a vsn fit
coefficients-method Class to contain result of a vsn fit
coerce-method Fit the vsn model
dim-method Class to contain result of a vsn fit
dim-method Class to contain input data and parameters for vsn functions
exprs-method Class to contain result of a vsn fit
justvsn Wrapper functions for vsn
kidney Intensity data for 1 cDNA slide with two adjacent tissue samples from a nephrectomy (kidney)
logLik-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-method Plot row standard deviations versus row means
meanSdPlot-methods Plot row standard deviations versus row means
ncol-method Class to contain result of a vsn fit
ncol-method Class to contain input data and parameters for vsn functions
normalize.AffyBatch.vsn Wrapper for vsn to be used as a normalization method with expresso
nrow-method Class to contain result of a vsn fit
nrow-method Class to contain input data and parameters for vsn functions
plotVsnLogLik Calculate the log likelihood and its gradient for the vsn model
predict-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
scalingFactorTransformation The transformation that is applied to the scaling parameter of the vsn model
show-method Class to contain result of a vsn fit
show-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-method Fit the vsn model
vsn2-methods Fit the vsn model
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
vsnrma Wrapper functions for vsn
[-method Class to contain result of a vsn fit
[-method Class to contain input data and parameters for vsn functions