oligo (version 1.36.1)

batch: The batch variable for the samples.

Description

Copy number estimates are susceptible to systematic differences between groups of samples that were processed at different times or by different labs. While 'batch' is often unknown, a useful surrogates is often the scan date of the arrays (e.g., the month of the calendar year) or the 96 well chemistry plate on which the samples were arrayed during lab processing.

Usage

batch(object)
batchNames(object)
batchNames(object) <- value

Arguments

object

An object of class CNSet.

value

For 'batchNames', the value must be a character string corresponding of the unique batch names.

Value

• The method 'batch' returns a character vector that has the same length as the number of samples in the CNSet object.

See Also

CNSet-class

Examples

a <- matrix(1:25, 5, 5)
colnames(a) <- letters[1:5]
object <- new("CNSet", alleleA=a, batch=rep("batch1", 5))
batch(object)
batchNames(object)