normalizeFeatures: Normalization of expression features
In iC10: A Copy Number and Expression-Based Classifier for Breast Tumours

Description Usage Arguments Details Value Note Author(s) References Examples

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

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

`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

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

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

As CONOR package is no longer maintained, the methods are not available temporarily. We will include more normalization methods in the next version of this package.

Oscar M Rueda

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.

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