bg.correct.LESN {affyPLM} | R Documentation

## LESN - Low End Signal is Noise Background corrections

### Description

This function background corrects PM probe data using LESN - Low End Signal is Noise concepts.

### Usage

    bg.correct.LESN(object,method = 2,baseline = 0.25, theta=4)

### Arguments

`object` | an `AffyBatch`
`method` | an integer code specifying which method to use
`baseline` | A baseline value to use
`theta` | A parameter used in the background correction process

### Details

This method will be more formally documented at a later date.

The basic concept is to consider that the lowest end of intensites is most likely just noise (and should be heavily corrected) and the highest end signals are most likely signal and should have little adjustment. Low end signals are made much smaller while high end signals get less adjustment relative adjustment.

### Value

An `AffyBatch`

### Author(s)

Ben Bolstad bolstad@stat.berkeley.edu

### References

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

### Examples

    data(affybatch.example)
    affybatch.example.bgcorrect <- bg.correct.LESN(affybatch.example)

[Package affyPLM version 1.3.3 Index]