nimblegenNorm: Function to compute scaled log-ratios

Description Usage Arguments Details Value Author(s) References

Description

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

Usage

1

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 May 20, 2017, 10:13 p.m.

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