normalizeRPPA: Normalizes data in an RPPA data list

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

Normalizes data in an RPPA data list

Description

Normalizes data in an RPPA data list. Four different normalization methods are provided: using externally measured protein concentration, signals from housekeeping proteins or protein dyes and row normalization.

Usage

normalizeRPPA(x, method = "row", normalizer = "housekeeping", useCol = "BCA",
writetable = F,vals="logged")

Arguments

x	List containing RPPA data set
method	character string: one of proteinDye,row, housekeeping,extValue
normalizer	character string describing the target in slidedescription that should be used for normalization using housekeeping
useCol	character string describing the column in sampledescription that should be used for normalization using the method extValue.
writetable	logical. If true data are exported as tab delimited text files to current working directory
vals	the data is returned at log2 scale with substracted normalizer value per default. If argument is set to native the median of the normalizer values is added after normalization and the data is returned at native scale.

Details

The function provides four different methods to normalize RPPA data to ensure that an optimal data quality. The default method row uses the expression matrix: after taking the logarithm the row median is substracted from each value of one row assuming that the median expression over all targets of one sample is representing total protein amount of the spots. For the method proteinDye arrays with the pattern protein in the target description are used for normalization. For every spotting run a separate protein slide is required. If the slides containing more than one array, the arrays will be normalized by the corresponding protein array. To use external protein assay data for normalization, a column containing the protein concentration has to be added to the sampledescription file. The name of this column is addressed via the useCol argument. To use any other target for normalization the method housekeeping can be used. The target for this method has to be addressed via the normalizer argument.

Value

expression	matrix with protein expression data
dummy	matrix with protein expression data
arraydescription	data frame with feature data
sampledescription	data frame with pheno data

Author(s)

Heiko Mannsperger <[e-mail]>

Examples

## Not run: 
	library(RPPanalyzer)
	data(dataI)
	dataI_bgcorr <- correctBG(dataI,method="normexp")
	dataIb <- pick.high.conc(dataI_bgcorr,highest="dilution")
	normRow <- normalizeRPPA(dataIb,method="row")
	normDye <- normalizeRPPA(dataIb,method="proteinDye")
	normPassay <- normalizeRPPA(dataIb,method="extValue",useCol="concentration")
	normHK <-  normalizeRPPA(dataIb,method="housekeeping",normalizer="housekeeping")

## End(Not run)

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