transformAffyData: Transform affy spot data to probabilities
In coreymhudson/AffyDistance: Affymetrix helper functions

Description Usage Arguments Value Author(s) Examples

View source: R/transformAffyData.R

This function takes an affy array and transforms the data to a probability that a given mRNA is found within a random experiment.

1	transformAffyData(affy.list)

affy.list

a list of filenames pointing to a set of affymetrix experiments.

transformedArray

A matrix of size (col=experiments, rows=spots, values=probabilities)

Corey M. Hudson <coreymhudson@gmail.com>

function(affy.list){
	ab <- ReadAffy(filenames=affy.list)
	geneNames <- geneNames(ab[,1])
	eset <- rma(ab)
	remove(ab)
	eIntensity <- exprs(eset)
	remove(eset)
	transformedAffy <- apply(eIntensity, 2, function(eIntensity){ s <- sum(eIntensity); v <- eIntensity/s; v})
	remove(eIntensity)
	return(transformedAffy)
  }