affyVstRma {lumi}R Documentation

Preprocess Affymetrix data by integrating VST with RMA method

Description

Preprocess Affymetrix data by integrating VST with RMA method

Usage

affyVstRma(afbatch, bgcorrect.method = "none", bgcorrect.param = list(), VST.param = list(), verbose = TRUE, ...)

Arguments

afbatch a vector of CEL file names or an AffyBatch object, see AffyBatch-class
bgcorrect.method the name of the background adjustment method
bgcorrect.param a list of parameters for bgcorrect.method (if needed/wanted)
VST.param a list of parameters for vst method
verbose logical value. If TRUE it writes out some messages.
... other parameters used by rma function

Details

This function basically integrates the VST (variance stabilizing transformation) transformation into the rma 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

expresso and vst


[Package lumi version 1.8.3 Index]