rmaaddon {bapred} | R Documentation |
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 |
affybatchtest |
object of class |
Details
This function uses code from the off-CRAN package docval
, version 1.0.
Value
The covariate matrix of the test data after addon normalization. Observations in rows, variables in columns.
Author(s)
Roman Hornung
References
Kostka, D., Spang, R. (2008). Microarray based diagnosis profits from better documentation of gene expression signatures. PLoS Computational Biology 4(2):e22, <doi: 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)
## End(Not run)
[Package bapred version 1.1 Index]