iC10 (version 2.0.2)

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"))

Value

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

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

Author

Oscar M Rueda

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

require(iC10TrainingData)
data(train.CN)
data(train.Exp)
features <- matchFeatures(Exp=train.Exp,
Exp.by.feat="probe", ref="hg18")
features <- normalizeFeatures(features, "scale")