preprocessTools: Tools for microarray preprocessing.

In jmacdon/oligo: Preprocessing tools for oligonucleotide arrays

Description

These are tools to preprocess microarray data. They include background correction, normalization and summarization methods.

Usage

backgroundCorrectionMethods()
normalizationMethods()
summarizationMethods()
backgroundCorrect(object, method=backgroundCorrectionMethods(), copy=TRUE, extra, subset=NULL, target='core', verbose=TRUE)
summarize(object, probes=rownames(object), method="medianpolish", verbose=TRUE, ...)
## S4 method for signature 'FeatureSet'
normalize(object, method=normalizationMethods(), copy=TRUE, subset=NULL,target='core', verbose=TRUE, ...)
## S4 method for signature 'matrix'
normalize(object, method=normalizationMethods(), copy=TRUE, verbose=TRUE, ...)
## S4 method for signature 'ff_matrix'
normalize(object, method=normalizationMethods(), copy=TRUE, verbose=TRUE, ...)
normalizeToTarget(object, targetDist, method="quantile", copy=TRUE, verbose=TRUE)

Arguments

object	Object containing probe intensities to be preprocessed.
method	String determining which method to use at that preprocessing step.
targetDist	Vector with the target distribution
probes	Character vector that identifies the name of the probes represented by the rows of object.
copy	Logical flag determining if data must be copied before processing (TRUE), or if data can be overwritten (FALSE).
subset	Not yet implemented.
target	One of the following values: 'core', 'full', 'extended', 'probeset'. Used only with Gene ST and Exon ST designs.
extra	Extra arguments to be passed to other methods.
verbose	Logical flag for verbosity.
...	Arguments to be passed to methods.

Details

Number of rows of object must match the length of probes.

Value

backgroundCorrectionMethods and normalizationMethods will return a character vector with the methods implemented currently.

backgroundCorrect, normalize and normalizeToTarget will return a matrix with same dimensions as the input matrix. If they are applied to a FeatureSet object, the PM matrix will be used as input.

The summarize method will return a matrix with length(unique(probes)) rows and ncol(object) columns.

Examples

ns <- 100
nps <- 1000
np <- 10
intensities <- matrix(rnorm(ns*nps*np, 8000, 400), nc=ns)
ids <- rep(as.character(1:nps), each=np)
bgCorrected <- backgroundCorrect(intensities)
normalized <- normalize(bgCorrected)
summarizationMethods()
expression <- summarize(normalized, probes=ids)
intensities[1:20, 1:3]
expression[1:20, 1:3]
target <- rnorm(np*nps)
normalizedToTarget <- normalizeToTarget(intensities, target)

if (require(oligoData) & require(pd.hg18.60mer.expr)){
  ## Example of normalization with real data
  data(nimbleExpressionFS)
  boxplot(nimbleExpressionFS, main='Original')
  for (mtd in normalizationMethods()){
    message('Normalizing with ', mtd)
    res <- normalize(nimbleExpressionFS, method=mtd, verbose=FALSE)
    boxplot(res, main=mtd)
  }
}

jmacdon/oligo documentation built on Aug. 11, 2020, 12:32 a.m.