nimblegenScale {Ringo} | R Documentation

## Function to compute scaled log-ratios

### Description

This function compute the scaled log-ratios from raw probe intensities, as done by Nimblegen for scaling of ChIP-chip data.

### Usage

    nimblegenScale(myRG, ...)

### Arguments

`myRG` | Object of class `RGList`
`...` | further arguments passed on to `tukey.biweight`

### Details

Nimblegen provides scaled log-ratios as normalized values for the probes. log.ratio = log2(R)-log2(G) scaled.ratio = log.ratio - tukey.biweight(log.ratio)

### Value

Return an `MAList`, with the M slot of the list holding the scaled log ratios.

### Author(s)

Joern Toedling

### References

for more details on the Tukey biweight estimator: Statistical Algorithms Description Document, 2002, Affymetrix.

[Package Ringo version 1.48.0 Index]