iC10 (version 1.5)

normalizeFeatures: Normalization of expression features

Description

Normalization of expression features. Several methods available in the package CONOR can be used.

Usage

normalizeFeatures(x, method=c("none", "scale"))

Arguments

x

An object result of a call to matchFeatures

method

Several methods are available: "none": No normalization is done "scale": Each expression feature is scaled to have zero mean and standard deviation 1

Value

A list of the same format as matchFeatures, but with train.Exp anfd Exp normalized.

Details

No further normalization is needed on the copy number, as log2 ratios are comparable between platforms.

References

Ali HR et al. Genome-driven integrated classification of breast cancer validated in over 7,500 samples. Genome Biology 2014; 15:431. Curtis et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 2012; 486:346-352.

Examples

# NOT RUN {
require(iC10TrainingData)
data(train.CN)
data(train.Exp)
features <- matchFeatures(Exp=train.Exp,
Exp.by.feat="probe", ref="hg18")
features <- normalizeFeatures(features, "scale")
# }