Variance stabilization and calibration for microarray data

Documentation for package ‘vsn’ version 3.38.0

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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