# Variance stabilization and calibration for microarray data

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

getIntensityMatrix | Extract a matrix of microarray intensities from various kinds of objects
kidney | Intensity data for 1 cDNA slide with two adjacent tissue samples from a nephrectomy (kidney)
log.na | Wrapper around the log() function that avoids warnings when negative values are presented
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
nchoosek | List all subsets of size k from n objects
normalize.AffyBatch.vsn | Wrapper for vsn to be used as a normalization method in the package affy
rowSds | Row standard deviation of a numeric array
sagmbAssess | Simulate data and assess vsn's parameter estimation
sagmbSimulateData | Simulate data and assess vsn's parameter estimation
sqr | Square of a numeric expression
vsn | Variance stabilization and calibration for microarray data.
vsnh | A function that transforms a matrix of microarray intensities
vsnPlotPar | Plot trajectories of calibration and transformation parameters for a vsn fit