bg.correct {affy}R Documentation

Background Correction

Description

Background corrects probe intensities in an object of class AffyBatch.

Usage

bg.correct(object, method, ...)

bg.correct.rma(object,...)
bg.correct.mas(object, griddim)
bg.correct.none(object, ...)

Arguments

object An object of class AffyBatch.
method A character that defines what background correction method will be used. Available methods are given by bg.correct.methods.
griddim grid dimension used for mas background estimate. The array is divided into griddm equal parts. Default is 16.
... arguments to pass along to the engine function.

Details

The name of the method to apply must be double-quoted. Methods provided with the package are currently: begin{itemize}

  • bg.correct.none: returns object unchanged.
  • bg.correct.chipwide: noise correction as described in a `white paper' from Affymetrix.
  • bg.correct.rma: the model based correction used by the RMA expression measure. end{itemize}

    They are listed in the variable bg.correct.methods. The user must supply the word after "bg.correct", i.e none, subtractmm, rma, etc...

    More details are available in the vignette.

    bg.correct.rma2 gives access to the older background method that was used by the rma function in version 1.1 bioconductor releases. For the 1.2 release rma performs the same background adjustment as bg.correct.rma. Unless you wish to duplicate older results in which case you should use bg.correct.rma.

    Details on the internal fucntions used by bg.correct.rma are in bg.adjust.

    Value

    An AffyBatch for which the intensities have been background adjusted. For some methods (RMA), only PMs are corrected and the MMs remain the same.

    Examples

        data(affybatch.example)
    
        ##bgc will be the bg corrected version of affybatch.example 
        bgc <- bg.correct(affybatch.example,method="rma") 
    
        ##This plot shows the tranformation
        plot(pm(affybatch.example)[,1],pm(bgc)[,1],log="xy",
            main="PMs before and after background correction")
    
    

    [Package affy version 1.8.1 Index]