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 toedling@ebi.ac.uk

See Also

tukey.biweight


[Package Ringo version 1.2.0 Index]