quantileNormalize: Quantile normalize a matrix

In aroneklund/bias: Visualize, Quantify, and Correct Technical Bias in Microarray Data

Description

Quantile normalize a matrix.

Usage

quantileNormalize(x, margin = 2)

Arguments

x	A numeric matrix.
margin	Margin over which to normalize (1 = rows, 2 = columns).

Details

Quantile normalization gives all columns (or rows, if margin=1) the same distribution.

Value

A numeric matrix of the same dimension as the input.

Note

Tied values within each column are placed in random order.

margin should be 2 for “standard” microarray matrices in which rows = genes.

See Also

normalize.quantiles in the affy package, normalizeQuantiles in the limma package.

Examples

  ## Not run: 
  library(affy)
  library(affydata)
  data(Dilution)
  d <- exprs(rma(Dilution))

  par(mfrow = c(1,2))
  plotDensity(d, main = '4 arrays: before...')
  plotDensity(quantileNormalize(d), 
    main = 'and after quantile normalization')

  
## End(Not run)

aroneklund/bias documentation built on May 10, 2019, 1:46 p.m.