BatchAdjust {SCAN.UPC}R Documentation

Helper function for applying the ComBat batch-adjusting methodology to an ExpressionSet object

Description

This is a convenience function for adjusting an ExpressionSet object for batch effects.

Usage

BatchAdjust(expressionSet, batchVariableName, covariateVariableNames=c())

Arguments

expressionSet

An ExpressionSet object that contains data to be adjusted for batch effects. This object should contain at least one phenoData column that indicates the batch number for each sample. Covariates may also be specified in other phenoData columns. Required.

batchVariableName

Name of phenoData column that indicates the batch number for each sample. Required.

covariateVariableNames

Name(s) of phenoData column(s) that indicate the covariate information for each sample. Optional.

Value

An ExpressionSet object indicating expression levels after batch adjustment.

Note

This function provides a convenient way to batch adjust an ExpressionSet object. It invokes the ComBat function within the sva package. Please see that package for additional details about how batch adjusting is performed. If multiple covariates are specified, a model matrix will be constructed that accounts for all covariates.

Author(s)

Stephen R. Piccolo

[Package SCAN.UPC version 2.24.1 Index]