affy (version 1.50.0)

preprocess: Background correct and Normalize

Description

This function pre-processes an AffyBatch.

Usage

preprocess(object, subset=NULL, normalize=TRUE, background=TRUE,
           background.method="RMA.2", normalize.method="quantile",
           background.param=list(), normalize.param=list(),
           verbosity.level=0)

Arguments

object

an AffyBatch

subset

a vector with the names of probesets to be used. If NULL then all probesets are used.

normalize

logical value. If TRUE normalize data using quantile normalization

background

logical value. If TRUE background correct using RMA background correction

background.method

name of background method to use.

normalize.method

name of normalization method to use.

background.param

list of parameters for background correction methods

normalize.param

list of parameters for normalization methods

verbosity.level

An integer specifying how much to print out. Higher values indicate more verbose. A value of 0 will print nothing

Value

• An AffyBatch

Details

This function carries out background correction and normalization pre-processing steps. It does not summarize to produce gene expression measures. All the same pre-processing methods supplied by threestep are supported by this function.

References

Bolstad, BM (2004) Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. PhD Dissertation. University of California, Berkeley.

See Also

expresso, rma

Examples

if (require(affydata)) {
  data(Dilution)

  # should be equivalent to the bg and norm of rma()
  abatch.preprocessed <- preprocess(Dilution)
}