frma (version 1.24.0)

frma: Frozen Robust Multi-Array Analysis

Description

This function preprocesses an AffyBatch, ExonFeatureSet, or GeneFeatureSet object using the fRMA method.

Usage

frma(object, background="rma", normalize="quantile", summarize="robust_weighted_average", target="probeset", input.vecs=NULL, output.param=NULL, verbose=FALSE)

Arguments

object

an AffyBatch, ExonFeatureSet, or GeneFeatureSet

background

type of background correction to perform: either "none" or "rma".

normalize

type of normalization to perform: either "none" or "quantile".

summarize

type of summarization to perform: one of "median\_polish", "average", "median", "weighted\_average", "robust\_weighted\_average", "random\_effect".

target

summarization level for exon and gene arrays. Must be one of: probeset, core, full (exon only), extended (exon only).

input.vecs

a list of vectors to be used in preprocessing. If NULL, the correct package with pre-made vectors is loaded if it has been installed. These packages are of the form: frmavecs.

output.param

a vector of output elements to return. By default only the expression values and standard errors (if applicable) are returned. Additional options are: "residuals", "weights", "random_effects"

verbose

logical value. If TRUE then some messages are displayed while the function runs.

Value

The function returns an ExpressionSet if output.param=NULL or an frmaExpressionSet otherwise.

Examples

  library(frmaExampleData)
  data(AffyBatchExample)
  object <- frma(AffyBatchExample)