norm.GC {mixer}R Documentation

Normalize 2-color array ChIP-chip data based on GC content

Description

Normalize are carried separatly for different GC content

Usage

norm.GC(x5, x3, nGC, method = c("lowess", "linear"), f=1/3, n.grp=500)

Arguments

x5 a vector of the log-transformed Cy5 (IP) data
x3 a vector of the log-transformed Cy3 Control) data
nGC a vector of the counts of G/C nucleotides in each probe, Note, it is asssumed that x5, x3 and nGC have the same order
method Two methods of normalizatoin, see details
f the parameter (fraction of data used) for lowess smoothing
n.grp the minimum number of probes within a GC group. If there are less than n.grp probes in one GC group, combine it with the group of similar GC content. Currently we assume only those groups with too big or too small GC content may have fewer probes than needed

Details

There are two methods of normalizations. Either by median regression, using function rq from R/quantreg or using lowess to fit the curve, and then take the residuals, divided by median absolute deviation.

Value

a vector of nomalized version of 'x5-x3'.

Author(s)

Wei Sun


[Package mixer version 1.03 Index]