correctBG: Corrects for background in an RPPA data set

In RPPanalyzer: Reads, Annotates, and Normalizes Reverse Phase Protein Array Data

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

Author(s)

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

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

## Not run: 
library(RPPanalyzer)
data(dataI)

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

## End(Not run)

RPPanalyzer documentation built on May 29, 2024, 5:43 a.m.