bkgdCorrect {codelink}R Documentation

Background correction of intensity values.

Description

Takes a Codelink object with Spot mean and Bkgd median values and corrects applying one of the methods available.

Usage

  bkgdCorrect(object, method = "half", preserve = FALSE, verbose = FALSE,
    offset = 0)

Arguments

object character; an object of class "Codelink".
method character; the correction method to use, one of "none", "subtract", "half" and "normexp".
preserve logical; if Smean and Bmedian slots should be preserved.
verbose logical; if TRUE print some information with method normexp.
offset numeric; value to add to intensities.

Details

Available methods are: . none: left intensities untouched. . subtract: simple subtraction of Bkgd median from Spot mean. . half: the same as above but aboid negative values setting all intensity values below zero to 0.5. . normexp: apply normexp background adjustment from package limma.

Value

An object of class Codelink with corrected intensity values, that is Ri slot.

Author(s)

Diego Diez

Examples

## Not run: 
    data(codelink.example)
    codelink.example <- bkgdCorrect(codelink.example, method = "half")
## End(Not run)

[Package codelink version 1.10.0 Index]