Entry: vsn
Aliases: class:vsn vsn-class [,vsn-method dim,vsn-method nrow,vsn-method ncol,vsn-method show,vsn-method exprs,vsn-method
Keywords: classes
Description: Class to contain result of a vsn fit
URL: ../../../library/vsn/html/class.vsn.html

Entry: vsnInput
Aliases: class:vsnInput vsnInput vsnInput-class [,vsnInput-method dim,vsnInput-method nrow,vsnInput-method ncol,vsnInput-method show,vsnInput-method
Keywords: classes
Description: Class to contain input data and parameters for vsn functions
URL: ../../../library/vsn/html/class.vsnInput.html

Entry: getIntensityMatrix
Aliases: getIntensityMatrix
Keywords: manip
Description: Extract a matrix of microarray intensities from various kinds of objects
URL: ../../../library/vsn/html/getIntensityMatrix.html

Entry: justvsn
Aliases: justvsn justvsn-methods justvsn,ExpressionSet-method justvsn,AffyBatch-method justvsn,RGList-method
Keywords: 
Description: Normalization with vsn
URL: ../../../library/vsn/html/justvsn.html

Entry: kidney
Aliases: kidney
Keywords: datasets
Description: Intensity data for 1 cDNA slide with two adjacent tissue samples from a nephrectomy (kidney)
URL: ../../../library/vsn/html/kidney.html

Entry: lymphoma
Aliases: lymphoma
Keywords: datasets
Description: Intensity data for 8 cDNA slides with CLL and DLBL samples from the Alizadeh et al. paper in Nature 2000
URL: ../../../library/vsn/html/lymphoma.html

Entry: meanSdPlot
Aliases: meanSdPlot meanSdPlot-methods meanSdPlot,matrix-method meanSdPlot,ExpressionSet-method meanSdPlot,vsn-method meanSdPlot,exprSet-method
Keywords: hplot methods
Description: Plot row standard deviations versus row means
URL: ../../../library/vsn/html/meanSdPlot.html

Entry: normalize.AffyBatch.vsn
Aliases: normalize.AffyBatch.vsn
Keywords: robust
Description: Wrapper for vsn to be used as a normalization method in the package affy
URL: ../../../library/vsn/html/normalize.AffyBatch.vsn.html

Entry: sagmbSimulateData
Aliases: sagmbSimulateData sagmbAssess
Keywords: datagen
Description: Simulate data and assess vsn's parameter estimation
URL: ../../../library/vsn/html/sagmbSimulateData.html

Entry: vsn
Aliases: vsn
Keywords: robust
Description: Variance stabilization and calibration for microarray data.
URL: ../../../library/vsn/html/vsn.html

Entry: vsn2
Aliases: vsn2 vsn2-methods vsn2,matrix-method vsn2,numeric-method vsn2,ExpressionSet-method vsnMatrix
Keywords: 
Description: Fit the vsn model
URL: ../../../library/vsn/html/vsn2.html

Entry: vsn2trsf
Aliases: vsn2trsf predict,vsn-method
Keywords: 
Description: Apply the vsn transformation to data
URL: ../../../library/vsn/html/vsn2trsf.html

Entry: logLik-methods
Aliases: logLik-methods logLik,vsnInput-method plotVsnLogLik
Keywords: 
Description: Calculate the log likelihood and its gradient for the vsn model
URL: ../../../library/vsn/html/vsnLikelihood.html

Entry: vsnPlotPar
Aliases: vsnPlotPar
Keywords: hplot
Description: Plot trajectories of calibration and transformation parameters for a vsn fit
URL: ../../../library/vsn/html/vsnPlotPar.html

Entry: vsnh
Aliases: vsnh
Keywords: 
Description: A function that transforms a matrix of microarray intensities
URL: ../../../library/vsn/html/vsnh.html
