normalize.exprSet: Normalization applied to ExpressionSets

In affyPLM: Methods for fitting probe-level models

Description

Allows the user to apply normalization routines to ExpressionSets.

Usage

  normalize.ExpressionSet.quantiles(eset, transfn=c("none","log","antilog"))
  normalize.ExpressionSet.loess(eset, transfn=c("none","log","antilog"),...)
  normalize.ExpressionSet.contrasts(eset, span = 2/3,
      choose.subset=TRUE, subset.size=5000, verbose=TRUE, family="symmetric",
      transfn=c("none","log","antilog")) 
  normalize.ExpressionSet.qspline(eset, transfn=c("none","log","antilog"),...)
  normalize.ExpressionSet.invariantset(eset,prd.td=c(0.003, 0.007),
      verbose=FALSE, transfn=c("none","log","antilog"),
      baseline.type=c("mean","median","pseudo-mean","pseudo-median")) 
  normalize.ExpressionSet.scaling(eset, trim=0.02, baseline=-1,
      transfn=c("none","log","antilog"))

Arguments

eset	An ExpressionSet
span	parameter to be passed to the function loess.
choose.subset	use a subset of values to establish the normalization relationship
subset.size	number to use for subset
verbose	verbosity flag
family	parameter to be passed to the function loess.
prd.td	cutoff parameter (details in the bibliographic reference)
trim	How much to trim from the top and bottom before computing the mean when using the scaling normalization
baseline	Index of array to use as baseline, negative values (-1,-2,-3,-4) control different baseline selection methods
transfn	Transform the ExpressionSet before normalizing. Useful when dealing with expression values that are log-scale
baseline.type	A method of selecting the baseline array
...	Additional parameters that may be passed to the normalization routine

Details

This function carries out normalization of expression values. In general you should either normalize at the probe level or at the expression value level, not both.

Typing normalize.ExpressionSet.methods should give you a list of methods that you may use. note that you can also use the normalize function on ExpressionSets. Use method to select the normalization method.

Value

A normalized ExpressionSet.

Author(s)

Ben Bolstad, [e-mail]

References

Bolstad, BM (2004) Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. PhD Dissertation. University of California, Berkeley.

Examples

if (require(affydata)) {
  data(Dilution)
  eset <- rma(Dilution, normalize=FALSE, background=FALSE)
  normalize(eset)
}

affyPLM documentation built on Nov. 8, 2020, 6:53 p.m.