codelink (version 1.40.2)

bkgdCorrect: Background correction of intensity values.

Description

Takes a CodelinkSet or Codelink object with Spot mean and Bkgd median values and performes background correction using one of the methods available.

Usage

bkgdCorrect(object, method = "half", preserve = FALSE, verbose = FALSE, offset = 0)
"codCorrect"(object, method = "half", normexp.method="saddle", offset=0)

Arguments

object

an object of class CodelinkSet or Codelink.

method

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.

normexp.method

method used with normexp correction.

offset

numeric; value to add to intensities.

Value

Ri slot.

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.

Examples

    data(codset)
    codset <- codCorrect(codset, method = "half")