bkgdCorrect: Background correction of intensity values.

In codelink: Manipulation of Codelink microarray data

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)

## S4 method for signature 'CodelinkSet'
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.

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

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

codelink documentation built on Nov. 8, 2020, 8:19 p.m.