This is a convenience function for adjusting an ExpressionSet object for batch effects.
Tab-separated text file that indicates batch (and optionally, covariate information) for each sample. Required.
An ExpressionSet object indicating expression levels after batch adjustment.
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.
Stephen R. Piccolo
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