affy: generateExprSet-methods – R documentation

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generateExprSet-methods

generate a set of expression values

Description

Generate a set of expression values from the probe pair information. The set of expression is returned as an ExpressionSet object.

Usage

computeExprSet(x, pmcorrect.method, summary.method, ...)

  generateExprSet.methods()

  upDate.generateExprSet.methods(x)

Arguments

`x`	a `AffyBatch` holding the probe level informations to generate the expression values, for computeExprSet, and for upDate.generateExprSet.methods it is a character vector..
`pmcorrect.method`	the method used to correct PM values (see section 'details').
`summary.method`	the method used to generate the expression value (see section 'details').
`...`	any of the options of the normalization you would like to modify.

Details

An extra argument ids= can be passed. It must be a vector of affids. The expression values will only be computed and returned for these affyids.

The different methods available through this mechanism can be accessed by calling the method generateExprSet.methods with an object of call Cel.container as an argument.

In the Affymetrix design, MM probes were included to measure the noise (or background signal). The original algorithm for background correction was to subtract the MM signal to the PM signal. The methods currently included in the package are "bg.correct.subtractmm", "bg.correct.pmonly" and "bg.correct.adjust".

To alter the available methods for generating ExprSets use upDate.generateExprSet.methods.

Examples

if (require(affydata)) {
  data(Dilution)

  ids <- c( "1000_at","1001_at")

  eset <- computeExprSet(Dilution, pmcorrect.method="pmonly",
                         summary.method="avgdiff", ids=ids)
}

affy

Methods for Affymetrix Oligonucleotide Arrays

v1.68.0

LGPL (>= 2.0)

Authors

Rafael A. Irizarry <rafa@ds.harvard.edu>, Laurent Gautier <lgautier@gmail.com>, Benjamin Milo Bolstad <bmb@bmbolstad.com>, and Crispin Miller <cmiller@picr.man.ac.uk> with contributions from Magnus Astrand <Magnus.Astrand@astrazeneca.com>, Leslie M. Cope <cope@mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad Halling <challing@agilixcorp.com>, Wolfgang Huber, James MacDonald <jmacdon@u.washington.edu>, Benjamin I. P. Rubinstein, Christopher Workman <workman@cbs.dtu.dk>, John Zhang

Initial release