RPPanalyzer (version 1.4.9)

correctBG: Corrects for background in an RPPA data set

Description

Corrects for background in an RPPA data set using different algorithms (e.g. from the limma package) avoiding negative values

Usage

correctBG(x, method = "normexp")

Value

expression

matrix with background corrected expression data

background

matrix with background data

arraydescription

data frame with feature data

sampledescription

data frame with pheno data

Arguments

x

List with RPPA data set

method

any method from the function backgroundCorrect and addmin which adds a fix number to each value to avoid negative values

Author

Heiko Mannsperger <[e-mail]>, Stephan Gade <[e-mail]>

Details

This function is a wrapper for the backgroundCorrect function of the limma package. As additional method "addmin" is implemented.

References

Ritchie, ME, Silver, J, Oshlack, A, Holmes, M, Diyagama, D, Holloway, A, and Smyth, GK (2007). A comparison of background correction methods for two-colour microarrays. Bioinformatics 23, 2700-2707.

See Also

For detailed information about the background correction methods see: backgroundCorrect,

Examples

if (FALSE) {
library(RPPanalyzer)
data(dataI)

dataBGcorrected <- correctBG(dataI,method="normexp")
}