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

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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

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

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