bgAdjust: Background adjustment for Illumina data

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Description

The method adjusts the data by subtracting an offset, which is estimated based on the quantile of the control probes

Usage

bgAdjust(lumiBatch, probs = 0.5, ...)

Arguments

lumiBatch	A LumiBatch object with controlData slot include control probe information
probs	The quantile used to estimate the background
...	other parameters used by quantile method

Details

The method adjusts the data by subtracting an offset, which is estimated based on the quantile of the control probes. The control probe information is kept in the controlData slot of the LumiBatch object. If no control data information, the method will do nothing.

Value

It returns a LumiBatch object with background adjusted.

Author(s)

Pan Du

See Also

lumiB

Examples

	data(example.lumi)
	## Here will assume the minimum of the control probe as the background,
	##    because there is no negative control (blank beads) information for the Barnes data.
	example.lumi.b <- bgAdjust(example.lumi, probs=0)

lumi documentation built on Nov. 8, 2020, 5:27 p.m.