BatchAdjustFromFile: Helper function for applying the ComBat batch-adjusting...

In SCAN.UPC: Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)

Description

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

Usage

BatchAdjustFromFile(expressionSet, batchFilePath)

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.
batchFilePath	Tab-separated text file that indicates batch (and optionally, covariate information) for each sample. Required.

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.

The batch file must contain a row for each of the samples in the ExpressionSet object, and one of the columns must use the name “batch” to indicate that the values represent batch number. The remaining column(s), if present, will be treated as covariates. If multiple covariates are specified, a model matrix will be constructed that accounts for all covariates.

Author(s)

Stephen R. Piccolo

SCAN.UPC documentation built on Nov. 8, 2020, 11:10 p.m.