bapred (version 1.1)

rmatrain: RMA normalization with ``documentation by value'' (Kostka & Spang, 2008)

Description

Performs RMA normalization and returns the normalized dataset together with information necessary for addon RMA normalization (Kostka & Spang, 2008) using rmaaddon.

Usage

rmatrain(affybatchtrain)

Arguments

affybatchtrain

object of class AffyBatch. Affymetrix GeneChip probe level data.

Value

rmatrain returns an object of class rmatrain. An object of class "rmatrain" is a list containing the following components:

xnorm

matrix of RMA normalized (training) data. Observations in rows, variables in columns.

rmadoc, sumdoc.rma, nfeature

information necessary for addon RMA normalization

Details

This function uses code from the off-CRAN package docval, version 1.0.

References

Kostka, D., Spang, R. (2008). Microarray based diagnosis profits from better documentation of gene expression signatures. PLoS Computational Biology 4(2):e22, <10.1371/journal.pcbi.0040022>.

Examples

# NOT RUN {
# Read in example data from ArrayExpress-webpage:

library("ArrayExpress")

expFiles <- getAE("E-GEOD-62837", path = tempdir(), type = "raw")

rawfiles <- file.path(tempdir(), expFiles$rawFiles)

library("affy")
# Training data:
affybatchtrain <- ReadAffy(filenames=rawfiles[1:3])

try(file.remove(file.path(tempdir(), expFiles$rawFiles)))
try(file.remove(file.path(tempdir(), expFiles$processedFiles)))
try(file.remove(file.path(tempdir(), expFiles$sdrf)))
try(file.remove(file.path(tempdir(), expFiles$idf)))
try(file.remove(file.path(tempdir(), expFiles$adf)))
try(file.remove(file.path(tempdir(), expFiles$rawArchive)))
try(file.remove(file.path(tempdir(), expFiles$processedArchive)))


# RMA normalization with documentation by value:
rmaparams <- rmatrain(affybatchtrain)
Xtrainnorm <- rmaparams$xnorm
dim(Xtrainnorm)
# }