correctBG {RPPanalyzer}R Documentation

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")

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

Details

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

Value

expression matrix with expression data
background matrix with background data
arraydescription data frame with feature data
sampledescription data frame with pheno data

Author(s)

Heiko Mannsperger <h.mannsperger@dkfz.de>, Stephan Gade <s.gade@dkfz.de>

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

        
library(RPPanalyzer)
data(dataI)

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


[Package RPPanalyzer version 1.0.2 Index]