RPPanalyzer (version 1.3)

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")

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

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

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

library(RPPanalyzer)
data(dataI)

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