bapred (version 1.1)

rmaaddon: Addon RMA normalization using ``documentation by value'' (Kostka & Spang, 2008)

Description

Performs RMA with addon quantile normalization by using documentation by value (Kostka & Spang, 2008).

Usage

rmaaddon(params, affybatchtest)

Arguments

params

object of class rmatrain. The normalized training data together with the information necesssary for addon normalization.

affybatchtest

object of class AffyBatch, that is Affymetrix GeneChip probe level data. Test data to be used for addon normalization.

Value

The covariate matrix of the test data after addon normalization. Observations in rows, variables in columns.

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])
# Test data:
affybatchtest <- ReadAffy(filenames=rawfiles[4:5])

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)

# RMA addon normalization:
Xtestaddonnorm <- rmaaddon(rmaparams, affybatchtest)
dim(Xtestaddonnorm)
# }