affyExpresso {lumi}R Documentation

Preprocess Affymetrix data by integrating VST with expresso method

Description

Preprocess Affymetrix data by integrating VST with expresso method

Usage

affyExpresso(afbatch, bg.correct = TRUE, bgcorrect.method = NULL, bgcorrect.param = list(), variance.stabilize = TRUE, varianceStabilize.method = c("vst", "log2", "cubicRoot"), varianceStabilize.param = list(), normalize = TRUE, normalize.method = NULL, normalize.param = list(), pmcorrect.method = NULL, pmcorrect.param = list(), summary.method = NULL, summary.param = list(), summary.subset = NULL, verbose = TRUE)

Arguments

afbatch a vector of CEL file names or an AffyBatch object, see AffyBatch-class
bg.correct a boolean to express whether background correction is wanted or not
bgcorrect.method the name of the background adjustment method
bgcorrect.param a list of parameters for bgcorrect.method (if needed/wanted)
variance.stabilize a boolean to express whether variance stabilization is wanted or not
varianceStabilize.method the name of the variance stabilizing transform, same as lumiT function
varianceStabilize.param a list of parameters for transformation method
normalize normalization step wished or not
normalize.method the normalization method to use
normalize.param a list of parameters to be passed to the normalization method (if wanted)
pmcorrect.method the name of the PM adjustement method
pmcorrect.param a list of parameters for pmcorrect.method (if needed/wanted)
summary.method the method used for the computation of expression values
summary.param a list of parameters to be passed to the summary.method (if wanted)
summary.subset a list of 'affyids'. If NULL, a expression summary value is computed for everything on the chip
verbose logical value. If TRUE it writes out some messages

Details

This function basically integrates the VST (variance stabilizing transformation) transformation into the expresso function in the affy package. The variance stabilization is based on the mean and variance relations of pixel intensities of each probe.

Value

Return an object of class ExpressionSet.

Note

The performance of this function is still under evaluation.

Author(s)

Pan Du

See Also

rma and vst


[Package lumi version 1.8.3 Index]