nimblegenNorm: Function to compute scaled log-ratios

In Ringo: R Investigation of ChIP-chip Oligoarrays

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.

Ringo documentation built on Nov. 8, 2020, 5:34 p.m.