ma.normalize: Microarray normalization

In fboulnois/made: Microarray Analysis of Differential Expression

Description

Background correct and normalize a microarray experiment.

Usage

ma.normalize(config)

Arguments

config

Character string consisting of the path to the configuration file generated using the write.yaml.config function or parsed configuration list associated with a microarray experiment.

Details

Reads in all the samples associated with a microarray experiment according to the options in the config and combines them using the Robust Multichip Average (RMA) algorithm, which background corrects, quantile normalizes, and summarizes the data using median polish at the level of probes in an expression set object (eset). If the option normalization: no is set in the config, an expression set is returned which has neither been background corrected nor normalized, a feature which is useful for quality assessment.

Value

Returns an expression set object that contains the microarray data at the level of probes.

References

Irizarry, Rafael A., Bridget Hobbs, Francois Collin, Yasmin D. Beazer-Barclay, Kristen J. Antonellis, Uwe Scherf, and Terence P. Speed. "Exploration, normalization, and summaries of high density oligonucleotide array probe level data." Biostatistics 4, no. 2 (2003): 249-264.

Carvalho, Benilton S., and Rafael A. Irizarry. "A framework for oligonucleotide microarray preprocessing." Bioinformatics 26, no. 19 (2010): 2363-2367.

See Also

write.yaml.config to generate the configuration file, and ma.summarize to convert an expression set object into a list of genes and their associated log-fold changes and statistical values.

Examples

if(require(madeData))
{
  config <- system.file("extdata", "config.yaml", package = "madeData")
  ma.normalize(config)
}

fboulnois/made documentation built on May 16, 2019, 12:01 p.m.